author	consortium	pmid	date	trait	efo	analysis	source	outcome	exposure	covariates	outcome_units	exposure_units	methylation_array	tissue	further_details	n	n_cohorts	age	sex	ethnicity	cpg	chrpos	chr	pos	gene	type	beta	se	p	details	study_id
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg07741821	chr7:26577897	7	26577897	KIAA0087	Open sea	-0.2909	0.02278	2.4e-37	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg12477880	chr21:36259241	21	36259241	RUNX1	Island	0.3916	0.03804	7.5e-25	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg02993069	chr1:36786777	1	36786777	C1orf113	Island	0.2031	0.01991	2.0000000000000002e-24	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg08882472	chr6:56607099	6	56607099	DST	Open sea	0.1456	0.0146	2.1e-23	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg17239923	chr11:128556611	11	128556611	-	North shelf	0.252	0.02538	3.1e-23	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg24942416	chr11:124621829	11	124621829	VSIG2	Open sea	-0.1773	0.01802	7.6e-23	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg02451831	chr7:26578098	7	26578098	KIAA0087	Open sea	-0.1673	0.01709	1.3e-22	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg07574178	chr5:80484747	5	80484747	RASGRF2	Open sea	-0.0758	0.00796	1.7e-21	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg00994804	chr21:36259383	21	36259383	RUNX1	Island	0.3941	0.04218	9.3e-21	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg11218872	chr3:193988737	3	193988737	-	South shore	-0.1187	0.01272	1.1e-20	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg03142697	chr21:36258497	21	36258497	RUNX1	North shore	0.4101	0.04473	4.8e-20	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg24999883	chr14:99880641	14	99880641	SETD3	Open sea	-0.0738	0.00805	5e-20	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg19765472	chr11:128556341	11	128556341	FLI1	North shelf	0.2199	0.02402	5.4e-20	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg08118908	chr16:15787920	16	15787920	NDE1	Open sea	-0.1006	0.01099	5.5e-20	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg08849601	chr2:135183637	2	135183637	MGAT5	Open sea	-0.081	0.00886	5.8e-20	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg04131721	chr10:121013657	10	121013657	GRK5	Open sea	-0.0962	0.01052	6.3e-20	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg02680932	chr1:110437204	1	110437204	-	Open sea	-0.0852	0.00934	6.9e-20	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg23565347	chr1:151672762	1	151672762	CELF3	Open sea	-0.1018	0.01117	8.2e-20	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg16831070	chr17:37721046	17	37721046	-	Open sea	-0.0685	0.00755	1.1e-19	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg01376763	chr16:81925132	16	81925132	PLCG2	Open sea	-0.0944	0.01046	1.8e-19	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg11972401	chr2:10830636	2	10830636	NOL10	South shore	0.0641	0.00712	2e-19	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg07841633	chr10:85363826	10	85363826	-	Open sea	-0.3058	0.03429	4.7e-19	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg11151981	chr3:16560711	3	16560711	-	Open sea	-0.0691	0.00777	6e-19	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg13382072	chr19:1851882	19	1851882	-	Island	0.1769	0.01994	7.2e-19	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg12679760	chr1:36786615	1	36786615	C1orf113	Island	0.1917	0.02166	9e-19	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg22539182	chr10:850393	10	850393	-	North shore	-0.1519	0.01734	2e-18	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg06758350	chr21:36259460	21	36259460	RUNX1	Island	0.2946	0.03367	2.1e-18	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg05042697	chr2:10830656	2	10830656	NOL10	South shore	0.0366	0.0042	2.8e-18	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg23719650	chr3:193988507	3	193988507	-	South shore	-0.1061	0.01217	3e-18	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg08730778	chr16:15787957	16	15787957	NDE1	Open sea	-0.1008	0.01161	3.6e-18	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg08898211	chr2:110970909	2	110970909	LINC00116	South shore	-0.0643	0.0074	3.8e-18	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg24020235	chr8:37575051	8	37575051	LOC101929622	Open sea	0.1701	0.01971	6.4e-18	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg21731862	chr10:15894004	10	15894004	FAM188A	Open sea	-0.078	0.00907	7.9e-18	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg19030331	chr11:7519636	11	7519636	OLFML1	Open sea	0.1575	0.01859	2.5e-17	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg22488975	chr1:184724009	1	184724009	EDEM3	Island	0.0176	0.00208	2.7e-17	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg11197061	chr3:96988343	3	96988343	EPHA6	Open sea	0.2406	0.02862	4.2e-17	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg12868449	chr13:99483755	13	99483755	DOCK9-AS1;DOCK9	Open sea	-0.1253	0.01499	6.4e-17	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg17831791	chr10:126712230	10	126712230	CTBP2	Island	-0.0868	0.01041	7.8e-17	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg11075561	chr6:36088380	6	36088380	-	Open sea	-0.2363	0.0285	1.1e-16	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg16026943	chr15:75641093	15	75641093	NEIL1	South shore	0.232	0.02834	2.7e-16	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg04599341	chr16:2029855	16	2029855	NOXO1	Island	0.1933	0.02364	3e-16	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg20418711	chr21:36259179	21	36259179	RUNX1	Island	0.2368	0.02921	5.2e-16	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg20606301	chr17:9571882	17	9571882	USP43	Open sea	-0.1625	0.02006	5.6e-16	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg11673291	chr1:36787145	1	36787145	-	Island	0.1736	0.02146	6.1e-16	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg14909179	chr11:882687	11	882687	CHID1	South shore	-0.2722	0.03394	0.0000000000000011	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg11824827	chr16:31075547	16	31075547	ZNF668	Island	-0.1402	0.01759	0.0000000000000016	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg03847470	chr11:128556580	11	128556580	FLI1	North shelf	0.2024	0.02541	0.0000000000000016	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg26974661	chr21:36258596	21	36258596	RUNX1	North shore	0.339	0.04261	0.0000000000000018	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg09777776	chr19:24269890	19	24269890	ZNF254	Open sea	0.0752	0.0095	0.0000000000000025	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg06721796	chr20:44037519	20	44037519	DBNDD2;SYS1-DBNDD2	South shore	0.0827	0.01045	0.0000000000000025	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg14937633	chr21:36259397	21	36259397	RUNX1	Island	0.22	0.02788	0.0000000000000029	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg08620751	chr19:1851750	19	1851750	-	Island	0.1314	0.01666	0.0000000000000031	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg05289022	chr2:98377864	2	98377864	TMEM131	Open sea	-0.1552	0.0197	0.0000000000000034	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg18062916	chr6:8839870	6	8839870	-	Open sea	-0.0987	0.01254	0.0000000000000036	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg02869559	chr21:36259067	21	36259067	RUNX1	Island	0.2475	0.03158	0.0000000000000046	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg11434705	chr19:1851995	19	1851995	-	Island	0.1725	0.02205	0.0000000000000053	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg05725197	chr2:237734577	2	237734577	-	Open sea	-0.1499	0.0193	0.0000000000000081	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg01521436	chr2:113542384	2	113542384	IL1A	Open sea	0.1033	0.01331	0.0000000000000084	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg20866256	chr12:2902218	12	2902218	-	North shore	-0.1395	0.01801	0.0000000000000096	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg24436531	chr11:128556352	11	128556352	FLI1	North shelf	0.2208	0.0288	0.000000000000018	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg12732514	chr17:77726237	17	77726237	-	South shelf	0.1243	0.01625	0.00000000000002	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg06361984	chr16:15787940	16	15787940	NDE1	Open sea	-0.1538	0.02014	0.000000000000022	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg26037180	chr14:88199948	14	88199948	-	Open sea	-0.2672	0.03512	0.000000000000028	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg14626029	chr6:130704336	6	130704336	TMEM200A	Open sea	-0.0852	0.01121	0.00000000000003	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg24179825	chr13:99483743	13	99483743	DOCK9-AS1;DOCK9	Open sea	-0.1225	0.01617	0.000000000000035	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg19896824	chr11:128555529	11	128555529	-	Open sea	0.225	0.02972	0.000000000000037	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg17349315	chr12:48188182	12	48188182	HDAC7	Open sea	-0.0881	0.01165	0.000000000000039	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg11883814	chr9:134756631	9	134756631	MED27	Open sea	-0.0688	0.00912	0.000000000000047	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg16932827	chr3:193988639	3	193988639	-	South shore	-0.0868	0.01155	0.000000000000055	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg17238473	chr2:98378600	2	98378600	TMEM131	Open sea	-0.0868	0.01156	0.000000000000058	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg14886629	chr3:10333655	3	10333655	GHRL;GHRLOS	Open sea	-0.128	0.01708	0.000000000000068	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg08853223	chr12:132021299	12	132021299	-	Open sea	-0.0689	0.00924	0.000000000000089	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg04204002	chr21:43817086	21	43817086	TMPRSS3	Open sea	-0.064	0.00859	0.00000000000009	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg18077307	chr2:98377791	2	98377791	TMEM131	Open sea	-0.2375	0.0319	0.000000000000097	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg11763830	chr17:72231400	17	72231400	TTYH2	Open sea	0.1417	0.01903	0.000000000000097	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg08900851	chr3:130558275	3	130558275	-	Open sea	0.1317	0.0177	0.000000000000098	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg03868978	chr21:42537294	21	42537294	-	North shelf	-0.0776	0.01051	0.00000000000015	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg17709804	chr11:128555749	11	128555749	-	Open sea	0.1285	0.01746	0.00000000000018	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg04283720	chr11:112834521	11	112834521	LOC101928847;NCAM1	South shore	0.1696	0.02309	0.0000000000002	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg21585414	chr21:31121163	21	31121163	GRIK1-AS1;GRIK1	Open sea	-0.1062	0.01451	0.00000000000025	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg02705918	chr12:114087236	12	114087236	-	Open sea	0.1504	0.02065	0.00000000000033	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg00194325	chr2:159940344	2	159940344	TANC1	Open sea	-0.0414	0.00569	0.00000000000037	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg06977984	chr15:52944386	15	52944386	FAM214A	Open sea	0.1853	0.02554	0.0000000000004	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg23198222	chr22:45071416	22	45071416	PRR5	Open sea	-0.1005	0.0139	0.00000000000048	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg02998028	chr2:135621153	2	135621153	ACMSD	Open sea	-0.1169	0.01619	0.00000000000052	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg13112407	chr2:97204931	2	97204931	ARID5A	South shore	-0.0675	0.00936	0.00000000000054	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg10542562	chr11:128556382	11	128556382	-	North shelf	0.1754	0.02435	0.00000000000058	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg02325250	chr5:131409289	5	131409289	CSF2	Open sea	-0.1036	0.01439	0.0000000000006	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg25589972	chr14:99829252	14	99829252	-	Open sea	-0.0862	0.01197	0.00000000000061	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg09547880	chr2:113542393	2	113542393	IL1A	Open sea	0.0876	0.0122	0.00000000000073	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg07491514	chr15:52944329	15	52944329	FAM214A	Open sea	0.1733	0.02417	0.00000000000077	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg13746740	chr11:128554939	11	128554939	-	Open sea	0.1669	0.02333	0.00000000000085	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg12306427	chr6:13428245	6	13428245	GFOD1	Open sea	-0.1318	0.01848	0.000000000001	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg04642306	chr11:112834466	11	112834466	NCAM1	Island	0.149	0.02101	0.0000000000013	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg22451408	chr21:45065904	21	45065904	HSF2BP	Open sea	-0.0767	0.01084	0.0000000000015	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg03335125	chr1:46088541	1	46088541	CCDC17	Island	-0.2076	0.02937	0.0000000000016	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg07163687	chr9:129767752	9	129767752	RALGPS1	Open sea	0.1017	0.0144	0.0000000000017	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg25054189	chr15:75641081	15	75641081	NEIL1	South shore	0.1195	0.01702	0.0000000000021	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg21929875	chr11:124622096	11	124622096	VSIG2	Open sea	-0.1547	0.02205	0.0000000000023	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg13006424	chr2:98377939	2	98377939	TMEM131	Open sea	-0.1763	0.02518	0.0000000000025	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg23497527	chr2:223269304	2	223269304	-	Open sea	0.0635	0.00908	0.0000000000027	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg05820020	chr14:35320834	14	35320834	BAZ1A	Open sea	-0.066	0.00946	0.000000000003	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg25552887	chr16:66751144	16	66751144	-	Open sea	-0.1156	0.01661	0.0000000000033	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg07989298	chr17:63074896	17	63074896	-	Open sea	-0.0776	0.01115	0.0000000000034	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg10820980	chr13:99483730	13	99483730	DOCK9-AS1;DOCK9	Open sea	-0.1324	0.01914	0.0000000000046	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg08516535	chr22:46001327	22	46001327	LINC01589	Open sea	-0.1085	0.01577	0.0000000000058	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg17944412	chr16:2029938	16	2029938	NOXO1	Island	0.1085	0.01579	0.0000000000062	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg07746249	chr10:68721801	10	68721801	LOC101928961;LRRTM3;CTNNA3	Open sea	-0.1614	0.0235	0.0000000000065	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg20008885	chr1:193670163	1	193670163	-	Open sea	-0.0967	0.01413	0.0000000000075	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg06687305	chr1:46088486	1	46088486	CCDC17	Island	-0.2212	0.03237	0.0000000000083	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg09889857	chr21:36259618	21	36259618	RUNX1	South shore	0.2443	0.03575	0.0000000000083	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg17766654	chr15:52944269	15	52944269	FAM214A	Open sea	0.2263	0.03311	0.0000000000083	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg02745221	chr14:99858359	14	99858359	-	Open sea	-0.1531	0.02244	0.0000000000087	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg02252742	chr16:89786500	16	89786500	ZNF276;VPS9D1	North shore	0.1121	0.01644	0.0000000000091	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg20337547	chr10:128990185	10	128990185	FAM196A;DOCK1	North shelf	-0.0553	0.00812	0.0000000000095	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg10490842	chr22:51016604	22	51016604	CPT1B;CHKB-CPT1B	Island	0.271	0.03983	0.00000000001	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg12226077	chr1:28641987	1	28641987	-	Open sea	-0.1816	0.02671	0.00000000001	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg03277268	chr7:151623360	7	151623360	-	Open sea	0.0918	0.01354	0.000000000012	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg21999471	chr11:128555317	11	128555317	-	Open sea	0.2825	0.04172	0.000000000013	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg02097604	chr17:17750910	17	17750910	TOM1L2	Open sea	-0.1051	0.01562	0.000000000017	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg08586366	chr11:128555301	11	128555301	-	Open sea	0.2324	0.03458	0.000000000018	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg07849827	chr1:15772154	1	15772154	CTRC	Open sea	-0.0935	0.01392	0.000000000019	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg27489873	chr2:217088135	2	217088135	-	Open sea	-0.1006	0.01503	0.000000000022	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg18478353	chr21:43986783	21	43986783	SLC37A1	North shelf	-0.0724	0.01086	0.000000000025	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg26890182	chr2:135621176	2	135621176	ACMSD	Open sea	-0.1166	0.01765	0.00000000004	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg16735956	chr6:36932863	6	36932863	-	South shelf	-0.0833	0.01263	0.000000000042	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg03952533	chr21:43679795	21	43679795	ABCG1	Open sea	-0.0765	0.01163	0.000000000048	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg00238508	chr3:71907737	3	71907737	-	Open sea	-0.128	0.01947	0.000000000049	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg07741929	chr21:45249962	21	45249962	-	South shelf	-0.0859	0.01308	0.00000000005	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg17942851	chr1:36786285	1	36786285	C1orf113	North shore	0.1264	0.01926	0.000000000052	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg05826295	chr6:113886340	6	113886340	-	Open sea	0.1725	0.02629	0.000000000054	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg01072045	chr11:47475796	11	47475796	-	Open sea	-0.07	0.01068	0.000000000056	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg07047831	chr3:186918647	3	186918647	RTP1	South shore	-0.0665	0.01015	0.000000000058	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg06871560	chr15:52944233	15	52944233	KIAA1370	Open sea	0.1674	0.02557	0.000000000058	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg09409898	chr17:2169829	17	2169829	SMG6	Open sea	-0.1462	0.02232	0.000000000058	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg11041353	chr10:97240141	10	97240141	SORBS1	Open sea	-0.0897	0.0137	0.000000000059	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg13754720	chr9:98274853	9	98274853	PTCH1	South shore	0.1601	0.02447	0.00000000006	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg05560127	chr11:128554774	11	128554774	-	Open sea	0.2307	0.03526	0.00000000006	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg11155658	chr3:49506751	3	49506751	DAG1	North shore	-0.0736	0.01126	0.000000000064	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg19664945	chr2:54087343	2	54087343	LOC100302652;GPR75	South shore	-0.2626	0.0402	0.000000000065	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg23463008	chr3:179598680	3	179598680	PEX5L	Open sea	-0.0434	0.00665	0.000000000067	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg11778548	chr1:155177963	1	155177963	MTX1;THBS3	North shore	0.0772	0.01182	0.000000000067	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg26570867	chr16:12308181	16	12308181	SNX29	Open sea	-0.105	0.01614	0.000000000078	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg11195375	chr11:124622348	11	124622348	VSIG2	Open sea	-0.1153	0.01772	0.000000000078	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg03897139	chr10:134018809	10	134018809	DPYSL4	North shore	-0.0689	0.01061	0.000000000083	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg00598394	chr12:93960818	12	93960818	-	North shelf	-0.0685	0.01055	0.000000000086	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg12172721	chr14:61822809	14	61822809	PRKCH	Open sea	0.1177	0.01815	0.000000000087	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg17139085	chr1:36787356	1	36787356	-	Island	0.1911	0.02947	0.000000000088	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg15852709	chr1:212611013	1	212611013	NENF	Open sea	-0.0548	0.00845	0.000000000089	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg15934191	chr6:98298775	6	98298775	-	Open sea	0.1296	0.02008	0.00000000011	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg00641679	chr8:94230311	8	94230311	-	Open sea	0.1572	0.02436	0.00000000011	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg08441138	chr11:128555233	11	128555233	-	Open sea	0.1848	0.02865	0.00000000011	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg12451530	chr2:54087209	2	54087209	LOC100302652;GPR75	Island	-0.1912	0.02968	0.00000000012	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg10137990	chr8:145137203	8	145137203	GPAA1	Island	0.088	0.01367	0.00000000012	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg12083928	chr21:36259623	21	36259623	RUNX1	South shore	0.2186	0.03399	0.00000000013	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg23865831	chr15:83980262	15	83980262	-	Open sea	0.1004	0.01564	0.00000000014	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg09072231	chr21:30744759	21	30744759	BACH1-IT2	Open sea	-0.0854	0.01329	0.00000000014	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg22743917	chr10:79264914	10	79264914	KCNMA1	Open sea	-0.104	0.01622	0.00000000014	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg01566472	chr15:75641171	15	75641171	NEIL1	South shore	0.1118	0.01745	0.00000000015	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg04348441	chr10:115955087	10	115955087	TDRD1	Open sea	-0.1237	0.01931	0.00000000015	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg12329423	chr4:7628455	4	7628455	SORCS2	Open sea	0.2011	0.0315	0.00000000017	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg15877601	chr5:17797535	5	17797535	-	Open sea	-0.0656	0.01026	0.00000000017	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg24069542	chr18:46469214	18	46469214	SMAD7	Open sea	-0.146	0.02288	0.00000000018	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg27496339	chr7:43803803	7	43803803	BLVRA	Open sea	0.186	0.02921	0.00000000019	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg25295723	chr10:134789042	10	134789042	-	North shore	-0.074	0.01162	0.00000000019	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg01635555	chr16:73101264	16	73101264	-	South shore	-0.0987	0.01554	0.00000000021	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg02197978	chr16:15796887	16	15796887	NDE1	Open sea	-0.0658	0.01035	0.00000000021	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg07844381	chr4:82342723	4	82342723	-	Open sea	0.0633	0.00998	0.00000000022	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg11615743	chr2:47382538	2	47382538	C2orf61	Open sea	-0.129	0.02031	0.00000000022	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg09424382	chr4:34735270	4	34735270	-	Open sea	-0.026	0.00411	0.00000000025	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg15097669	chr12:56225116	12	56225116	TMEM198B	South shore	0.0856	0.01354	0.00000000026	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg23976034	chr7:69790830	7	69790830	AUTS2	Open sea	0.1097	0.01736	0.00000000026	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg19961545	chr2:54087066	2	54087066	GPR75;LOC100302652	Island	-0.1754	0.02782	0.00000000029	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg00891669	chr4:26814011	4	26814011	-	Open sea	-0.1019	0.01617	0.00000000029	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg17983064	chr5:131396357	5	131396357	IL3	Open sea	-0.1213	0.01927	0.0000000003	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg24155444	chr1:155177969	1	155177969	MTX1;THBS3	North shore	0.0597	0.0095	0.00000000034	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg16181315	chr1:6687052	1	6687052	THAP3	South shore	-0.0776	0.01238	0.00000000035	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg10040866	chr15:72690640	15	72690640	TMEM202	Open sea	0.0816	0.01301	0.00000000036	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg13745832	chr17:15405942	17	15405942	FAM18B2	Open sea	-0.17	0.0271	0.00000000036	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg14405300	chr2:88427027	2	88427027	FABP1	Open sea	-0.0694	0.01107	0.00000000037	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg24158028	chr10:134073307	10	134073307	STK32C	South shore	-0.0651	0.01039	0.00000000037	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg15856419	chr21:39760881	21	39760881	ERG	Open sea	-0.0877	0.01399	0.00000000037	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg01332683	chr16:16190393	16	16190393	ABCC1	Open sea	0.1323	0.02112	0.00000000038	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg13461447	chr1:1714001	1	1714001	-	Island	-0.1366	0.02182	0.00000000039	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg03724062	chr1:214746876	1	214746876	-	Open sea	0.0966	0.01544	0.00000000039	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg23799091	chr11:75365642	11	75365642	MAP6	Open sea	-0.109	0.01744	0.00000000041	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg10770023	chr22:51016644	22	51016644	CPT1B;CHKB-CPT1B	Island	0.3224	0.0517	0.00000000045	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg08611810	chr2:54087178	2	54087178	LOC100302652;GPR75	Island	-0.155	0.02487	0.00000000046	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg21210529	chr5:137588237	5	137588237	GFRA3	Open sea	-0.0581	0.00932	0.00000000047	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg09045689	chr2:31613833	2	31613833	XDH	Open sea	-0.0296	0.00475	0.00000000047	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg20488281	chr12:119772354	12	119772354	CCDC60	Island	0.1094	0.01757	0.00000000048	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg15238694	chr12:119740840	12	119740840	LOC144742	Open sea	0.1435	0.02307	0.0000000005	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg08257445	chr2:109997350	2	109997350	SH3RF3	Open sea	-0.0986	0.01585	0.0000000005	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg23097155	chr12:133066069	12	133066069	FBRSL1	Island	0.038	0.00613	0.00000000055	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg03920999	chr3:10334760	3	10334760	GHRLOS;GHRL	Open sea	-0.0481	0.00775	0.00000000057	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg07032852	chr9:140068071	9	140068071	-	North shore	0.0893	0.01443	0.00000000061	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg18522909	chr2:47382903	2	47382903	C2orf61	Open sea	-0.125	0.0202	0.00000000062	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg10316525	chr15:40572137	15	40572137	-	Island	-0.2162	0.035	0.00000000065	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg01876338	chr2:54087008	2	54087008	GPR75;LOC100302652	Island	-0.212	0.03435	0.00000000068	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg04790209	chr2:7274020	2	7274020	-	Open sea	-0.0917	0.01486	0.00000000069	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg00518702	chr6:113886046	6	113886046	-	Open sea	0.1025	0.01663	0.0000000007	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg19313959	chr12:2902708	12	2902708	FKBP4	North shore	-0.1464	0.02375	0.00000000071	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg21532590	chr3:125903636	3	125903636	ALDH1L1-AS2	Open sea	0.0683	0.01109	0.00000000073	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg08186548	chr8:95139521	8	95139521	CDH17	Open sea	-0.059	0.00958	0.00000000074	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg10801420	chr3:9944591	3	9944591	IL17RE	Open sea	-0.1364	0.02216	0.00000000074	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg13860849	chr11:66084469	11	66084469	CD248	Island	0.0954	0.0155	0.00000000076	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg13985132	chr15:65394414	15	65394414	LOC390595	Island	-0.222	0.03614	0.0000000008	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg13338289	chr10:30331680	10	30331680	KIAA1462	Open sea	-0.0721	0.01175	0.00000000083	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg12131208	chr17:58499700	17	58499700	C17orf64	South shore	0.1757	0.02863	0.00000000084	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg03119829	chr1:64170964	1	64170964	-	Open sea	0.1388	0.02263	0.00000000086	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg13942119	chr12:13326748	12	13326748	-	Open sea	0.0773	0.01262	0.00000000089	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg17952465	chr22:51016839	22	51016839	CPT1B;CHKB-CPT1B	Island	0.2409	0.03936	0.00000000094	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg24363820	chr22:51016703	22	51016703	CPT1B;CHKB-CPT1B	Island	0.3158	0.05164	0.00000000096	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg23218897	chr17:2169522	17	2169522	SMG6	Open sea	-0.1195	0.01956	0.00000000098	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg19979370	chr11:128772355	11	128772355	KCNJ5;C11orf45	Open sea	-0.1227	0.0201	0.000000001	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg11240129	chr1:46088617	1	46088617	CCDC17	Island	-0.1798	0.02945	0.000000001	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg09423021	chr1:226960554	1	226960554	-	Open sea	-0.072	0.0118	0.000000001	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg17403995	chr1:52348865	1	52348865	-	South shelf	0.0751	0.01232	0.0000000011	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg01432055	chr3:124873848	3	124873848	SLC12A8	Open sea	-0.0514	0.00845	0.0000000011	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg01590762	chr6:121914368	6	121914368	-	Open sea	0.1557	0.02553	0.0000000011	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg15768040	chr9:98222052	9	98222052	PTCH1	Open sea	0.2036	0.03337	0.0000000011	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg07277559	chr5:71814028	5	71814028	-	Open sea	0.116	0.01905	0.0000000011	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg24238305	chr6:165959578	6	165959578	PDE10A	Open sea	-0.0292	0.0048	0.0000000011	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg22928020	chr21:39616836	21	39616836	KCNJ15	Open sea	-0.0754	0.01237	0.0000000011	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg10080808	chr8:37574987	8	37574987	LOC101929622	Open sea	0.085	0.01395	0.0000000011	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg05381578	chr4:152595994	4	152595994	GATB	Open sea	-0.1273	0.02094	0.0000000012	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg14133557	chr9:113802005	9	113802005	-	South shore	-0.1697	0.02798	0.0000000013	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg27131667	chr16:89619402	16	89619402	SPG7	Open sea	-0.0679	0.0112	0.0000000013	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg23517074	chr21:35238658	21	35238658	ITSN1	Open sea	-0.0791	0.01304	0.0000000013	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg03400002	chr9:94266072	9	94266072	-	Open sea	0.0482	0.00794	0.0000000013	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg09502619	chr16:1609529	16	1609529	IFT140	Open sea	-0.0749	0.01237	0.0000000014	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg01210965	chr3:126259452	3	126259452	CHST13;C3orf22	North shore	0.0872	0.0144	0.0000000014	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg03516335	chr11:72122809	11	72122809	CLPB	Open sea	0.0558	0.00923	0.0000000015	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg07890839	chr15:67359525	15	67359525	SMAD3	South shore	0.088	0.01456	0.0000000015	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg03996581	chr1:153586386	1	153586386	S100A16	Open sea	-0.0865	0.01433	0.0000000015	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg19143959	chr15:40572794	15	40572794	-	North shore	-0.1268	0.021	0.0000000016	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg04413853	chr17:58499706	17	58499706	C17orf64	South shore	0.1201	0.01988	0.0000000016	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg13483727	chr18:615471	18	615471	CLUL1	Open sea	0.1219	0.02023	0.0000000017	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg23713900	chr18:615496	18	615496	CLUL1	Open sea	0.1047	0.01739	0.0000000017	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg11287187	chr12:133413532	12	133413532	-	South shore	-0.2347	0.03894	0.0000000017	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg23872513	chr11:112885708	11	112885708	NCAM1	Open sea	-0.1028	0.01707	0.0000000017	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg12912394	chr11:35835713	11	35835713	-	Open sea	-0.0295	0.00489	0.0000000017	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg14727981	chr6:37074912	6	37074912	-	Open sea	-0.0939	0.01559	0.0000000017	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg18891081	chr2:47382427	2	47382427	C2orf61	Open sea	-0.0715	0.01189	0.0000000018	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg19112186	chr22:51016638	22	51016638	CPT1B;CHKB-CPT1B	Island	0.3564	0.05924	0.0000000018	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg10692519	chr21:40342778	21	40342778	-	Open sea	-0.0706	0.01178	0.0000000021	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg08787837	chr16:86029554	16	86029554	-	Open sea	0.1243	0.02077	0.0000000022	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg13863153	chr21:39628679	21	39628679	KCNJ15	Open sea	-0.0992	0.01658	0.0000000022	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg10409832	chr2:98376193	2	98376193	TMEM131	Open sea	-0.0626	0.01047	0.0000000022	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg07883622	chr12:62998134	12	62998134	C12orf61	South shore	0.0689	0.01154	0.0000000023	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg02232863	chr1:207243939	1	207243939	PFKFB2	Open sea	-0.0661	0.01106	0.0000000023	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg16291204	chr11:112885688	11	112885688	NCAM1	Open sea	-0.1011	0.01694	0.0000000024	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg24112628	chr6:150174215	6	150174215	LRP11	Open sea	-0.1338	0.02249	0.0000000027	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg02904657	chr15:40571997	15	40571997	-	North shore	-0.2234	0.03756	0.0000000027	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg10573232	chr12:119772533	12	119772533	CCDC60	Island	0.2093	0.03518	0.0000000027	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg22510139	chr1:3058822	1	3058822	PRDM16	North shore	0.1032	0.01737	0.0000000029	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg23715045	chr11:124621944	11	124621944	VSIG2	Open sea	-0.1304	0.02198	0.0000000029	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg00983520	chr22:51017067	22	51017067	CPT1B;CHKB-CPT1B	South shore	0.203	0.03428	0.0000000032	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg15581537	chr7:23375935	7	23375935	IGF2BP3	Open sea	0.1534	0.02592	0.0000000033	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg00966672	chr21:45329952	21	45329952	AGPAT3	Open sea	-0.0679	0.01147	0.0000000033	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg01145054	chr21:47063285	21	47063285	-	Island	-0.0073	0.00123	0.0000000035	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg12118986	chr19:39074494	19	39074494	RYR1	Open sea	-0.1119	0.01898	0.0000000037	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg08096851	chr17:77726257	17	77726257	-	South shelf	0.168	0.02854	0.0000000039	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg22586493	chr2:110014556	2	110014556	SH3RF3	Open sea	-0.109	0.01853	0.000000004	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg19085407	chr10:135164596	10	135164596	PRAP1	Open sea	0.1121	0.01906	0.0000000041	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg23757461	chr18:55924888	18	55924888	NEDD4L	South shore	0.0662	0.01128	0.0000000044	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg07339118	chr6:169251967	6	169251967	-	Open sea	0.0488	0.00833	0.0000000047	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg17281206	chr9:110837383	9	110837383	-	Open sea	-0.0682	0.01165	0.0000000048	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg26188212	chr1:228967124	1	228967124	-	Open sea	-0.1428	0.0244	0.0000000049	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg07042301	chr14:104338807	14	104338807	-	Open sea	-0.0598	0.01024	0.0000000051	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg21891597	chr8:132936123	8	132936123	EFR3A	Open sea	0.1345	0.02301	0.0000000051	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg06813295	chr21:46946981	21	46946981	SLC19A1	North shelf	-0.0314	0.00538	0.0000000055	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg01057898	chr22:19706868	22	19706868	SEPT5;SEPT5-GP1BB	South shore	0.0837	0.01435	0.0000000055	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg21122199	chr17:58499720	17	58499720	C17orf64	South shore	0.0897	0.0154	0.0000000057	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg14251734	chr10:100407378	10	100407378	HPSE2	Open sea	0.1272	0.02185	0.0000000058	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg23016776	chr10:99081496	10	99081496	FRAT1	South shore	0.0843	0.01448	0.0000000059	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg07127410	chr22:29427851	22	29427851	ZNRF3	South shore	-0.128	0.022	0.000000006	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg05156901	chr22:51016646	22	51016646	CPT1B;CHKB-CPT1B	Island	0.3283	0.05647	0.0000000061	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg06530441	chr22:51016950	22	51016950	CPT1B;CHKB-CPT1B	Island	0.2794	0.04807	0.0000000062	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg25857090	chr21:46975435	21	46975435	-	Island	-0.015	0.00259	0.0000000066	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg01517789	chr10:108342212	10	108342212	SORCS1	Open sea	0.0723	0.01249	0.0000000072	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg13609948	chr22:29427709	22	29427709	ZNRF3-AS1;ZNRF3	South shore	-0.1286	0.02225	0.0000000075	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg09152042	chr6:33383065	6	33383065	PHF1	North shelf	-0.0909	0.01575	0.0000000079	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg20258698	chr7:47556811	7	47556811	TNS3	Open sea	-0.172	0.02981	0.0000000079	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg23636331	chr4:16087132	4	16087132	-	South shore	-0.0718	0.01245	0.0000000081	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg20079298	chr15:40572326	15	40572326	-	Island	-0.2486	0.04313	0.0000000082	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg21023025	chr5:154172209	5	154172209	LARP1	Open sea	-0.0699	0.01214	0.0000000085	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg25451345	chr1:110709053	1	110709053	SLC6A17	Open sea	-0.0719	0.01248	0.0000000085	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg00195322	chr20:48278559	20	48278559	B4GALT5	Open sea	-0.0962	0.0167	0.0000000086	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg14023398	chr4:40633068	4	40633068	RBM47	South shore	0.0894	0.01554	0.0000000086	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg18468041	chr10:851101	10	851101	-	Island	-0.0808	0.01405	0.0000000088	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg27613645	chr1:155177659	1	155177659	MTX1;THBS3	North shore	0.0577	0.01002	0.0000000088	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg15350922	chr12:46054221	12	46054221	-	Open sea	0.0933	0.01624	0.0000000089	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg06746154	chr8:145137177	8	145137177	GPAA1	Island	0.0451	0.00786	0.0000000096	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg16059978	chr11:2308487	11	2308487	-	Open sea	0.161	0.02805	0.0000000096	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg11106793	chr2:103106125	2	103106125	SLC9A4	Open sea	-0.12	0.02095	0.00000001	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg06752482	chr17:58499816	17	58499816	C17orf64	South shore	0.0668	0.01169	0.000000011	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg08260245	chr22:51016501	22	51016501	CPT1B;CHKB-CPT1B	Island	0.3325	0.05827	0.000000012	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg25655189	chr14:78609989	14	78609989	-	Open sea	0.1601	0.02806	0.000000012	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg12622863	chr14:95712746	14	95712746	CLMN	Open sea	-0.0801	0.01405	0.000000012	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg05414908	chr2:54087173	2	54087173	LOC100302652;GPR75	Island	-0.1127	0.01981	0.000000013	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg09616647	chr3:183959171	3	183959171	VWA5B2;MIR1224	Island	0.1315	0.02313	0.000000013	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg03850117	chr16:87894334	16	87894334	SLC7A5	North shore	0.0574	0.01009	0.000000013	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg24624845	chr16:10974218	16	10974218	CIITA	South shore	0.0782	0.01375	0.000000013	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg22866426	chr21:36263347	21	36263347	RUNX1	Island	0.1654	0.02914	0.000000014	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg01920382	chr1:60196606	1	60196606	FGGY	Open sea	0.1049	0.01848	0.000000014	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg03865018	chr1:20031012	1	20031012	TMCO4	Open sea	-0.0868	0.01529	0.000000014	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg00751179	chr2:158695297	2	158695297	ACVR1	Open sea	0.0629	0.01107	0.000000014	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg19878627	chr2:54087184	2	54087184	LOC100302652;GPR75	Island	-0.1244	0.02197	0.000000015	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg17680767	chr5:73623208	5	73623208	-	Open sea	-0.1044	0.01845	0.000000015	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg06808571	chr7:150642256	7	150642256	KCNH2	North shelf	0.0884	0.01561	0.000000015	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg00173498	chr8:61912461	8	61912461	-	Open sea	0.0471	0.00832	0.000000015	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg02393727	chr16:89690088	16	89690088	DPEP1	Open sea	0.1605	0.02844	0.000000016	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg13889950	chr3:177076825	3	177076825	-	Open sea	-0.0611	0.01082	0.000000016	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg08975915	chr12:90050928	12	90050928	ATP2B1	Open sea	0.0959	0.017	0.000000017	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg14035368	chr9:139258938	9	139258938	CARD9;DNLZ	Island	0.1715	0.0305	0.000000019	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg15074613	chr17:48604896	17	48604896	MYCBPAP	Open sea	0.0666	0.01186	0.000000019	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg25400597	chr5:52542324	5	52542324	-	Open sea	-0.2479	0.04408	0.000000019	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg00598195	chr16:61922094	16	61922094	CDH8	Open sea	0.1231	0.02191	0.000000019	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg11828983	chr14:104734272	14	104734272	-	Open sea	0.1656	0.02949	0.00000002	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg00226815	chr3:47029143	3	47029143	NBEAL2	Open sea	-0.0734	0.01308	0.00000002	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg05210804	chr6:33282896	6	33282896	ZBTB22;TAPBP	Island	0.1827	0.0326	0.000000021	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg09856696	chr19:16540019	19	16540019	EPS15L1	Open sea	-0.0895	0.01597	0.000000021	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg08364093	chr2:28114164	2	28114164	BRE;RBKS;LOC100302650	South shore	0.0583	0.01042	0.000000022	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg24123198	chr4:184018031	4	184018031	-	North shore	0.1377	0.0246	0.000000022	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg05899103	chr15:65394570	15	65394570	LOC390595	Island	-0.1783	0.03189	0.000000022	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg27502912	chr22:51017001	22	51017001	CPT1B;CHKB-CPT1B	Island	0.2353	0.04208	0.000000022	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg01237541	chr10:85306289	10	85306289	-	Open sea	0.1656	0.02961	0.000000022	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg21545762	chr3:183959118	3	183959118	VWA5B2;MIR1224	Island	0.1406	0.02516	0.000000023	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg27003765	chr6:31846769	6	31846769	SLC44A4	Open sea	0.1059	0.01895	0.000000023	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg01964774	chr21:39663949	21	39663949	KCNJ15	Open sea	-0.0628	0.01124	0.000000023	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg03446062	chr6:14477353	6	14477353	-	Open sea	0.1178	0.02111	0.000000024	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg25468618	chr8:144810034	8	144810034	FAM83H	Island	0.176	0.03153	0.000000024	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg06438724	chr15:49089383	15	49089383	CEP152	Open sea	-0.1426	0.02556	0.000000024	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg19904322	chr21:45249837	21	45249837	-	South shelf	-0.0603	0.01081	0.000000025	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg10712211	chr8:70845033	8	70845033	-	Open sea	0.0882	0.01583	0.000000025	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg14886850	chr14:75122289	14	75122289	-	Open sea	-0.0938	0.01684	0.000000026	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg26983198	chr11:1952756	11	1952756	TNNT3	South shelf	0.1039	0.01869	0.000000027	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg02172058	chr17:58499911	17	58499911	C17orf64	South shore	0.1026	0.01846	0.000000027	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg14561362	chr4:146461062	4	146461062	SMAD1	Open sea	0.0751	0.01353	0.000000028	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg19696491	chr15:78857124	15	78857124	CHRNA5	North shore	-0.1179	0.02128	0.00000003	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg02197387	chr20:62694005	20	62694005	TCEA2	Island	0.094	0.01697	0.00000003	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg24049884	chr10:102667200	10	102667200	-	Open sea	-0.0639	0.01154	0.000000031	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg08297686	chr14:68943486	14	68943486	RAD51L1	Open sea	0.0583	0.01054	0.000000032	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg13813008	chr9:98428936	9	98428936	-	Open sea	0.1572	0.02844	0.000000032	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg12972300	chr15:70977671	15	70977671	UACA	Open sea	-0.0687	0.01243	0.000000032	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg02727835	chr11:45940878	11	45940878	PEX16	South shore	-0.063	0.01142	0.000000033	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg04638395	chr11:74892693	11	74892693	SLCO2B1	Open sea	0.0742	0.01343	0.000000033	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg09036297	chr10:134819166	10	134819166	-	North shelf	-0.0764	0.01385	0.000000034	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg03729276	chr10:112865659	10	112865659	-	Open sea	0.104	0.01883	0.000000034	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg02978008	chr2:47382666	2	47382666	C2orf61	Open sea	-0.0722	0.01309	0.000000035	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg09169132	chr2:171826682	2	171826682	-	North shelf	-0.0614	0.01115	0.000000036	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg14309283	chr6:33282890	6	33282890	ZBTB22;TAPBP	Island	0.1353	0.02455	0.000000036	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg07286682	chr15:69447132	15	69447132	MIR548H4	Open sea	0.1071	0.01944	0.000000036	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg00017931	chr6:157932180	6	157932180	ZDHHC14	Open sea	-0.0986	0.01791	0.000000037	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg27462685	chr13:75129579	13	75129579	LINC00347	Open sea	-0.1565	0.02844	0.000000037	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg10330057	chr1:203005307	1	203005307	-	Open sea	-0.0622	0.01132	0.000000038	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg22197811	chr22:38627189	22	38627189	TMEM184B	Open sea	-0.1542	0.02812	0.000000042	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg00701946	chr2:54087200	2	54087200	LOC100302652;GPR75	Island	-0.1444	0.02637	0.000000044	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg00443981	chr17:58499679	17	58499679	C17orf64	South shore	0.1276	0.02331	0.000000044	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg00362690	chr15:69447139	15	69447139	MIR548H4	Open sea	0.1447	0.02643	0.000000044	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg01586330	chr9:140067764	9	140067764	TMEM210	North shore	0.0759	0.01389	0.000000046	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg00718518	chr5:171766029	5	171766029	SH3PXD2B	North shore	-0.0827	0.01514	0.000000047	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg12761707	chr21:43468534	21	43468534	-	Open sea	-0.0676	0.01238	0.000000047	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg10606725	chr21:42551825	21	42551825	PLAC4;BACE2	Open sea	-0.0557	0.01021	0.000000048	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg26827202	chr2:196439116	2	196439116	-	Open sea	0.0806	0.01475	0.000000048	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg16487474	chr8:49496045	8	49496045	LOC101929268	Open sea	0.1557	0.02851	0.000000048	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg03192897	chr1:170115351	1	170115351	METTL11B	Open sea	0.1461	0.0268	0.000000049	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg25565476	chr7:106270744	7	106270744	-	Open sea	0.095	0.01745	0.000000051	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg20594465	chr13:58246705	13	58246705	PCDH17	Open sea	-0.0613	0.01125	0.000000051	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg00764652	chr21:42733397	21	42733397	MX2	Open sea	-0.0431	0.00792	0.000000051	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg04094640	chr16:27237122	16	27237122	NSMCE1	Open sea	-0.0614	0.01128	0.000000053	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg08381798	chr22:29705045	22	29705045	GAS2L1	South shore	-0.0682	0.01254	0.000000053	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg06390490	chr22:38627184	22	38627184	TMEM184B	Open sea	-0.1712	0.03147	0.000000053	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg12176783	chr20:62694000	20	62694000	TCEA2	Island	0.164	0.03017	0.000000055	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg23266308	chr3:9944212	3	9944212	IL17RE	Open sea	-0.0874	0.0161	0.000000056	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg19190699	chr15:101514156	15	101514156	LRRK1	Island	-0.0788	0.01454	0.00000006	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg21033715	chr21:28216125	21	28216125	ADAMTS1	North shore	-0.0057	0.00105	0.000000065	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg02314852	chr6:111532870	6	111532870	SLC16A10	Open sea	0.1391	0.02573	0.000000065	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg26024874	chr18:54541128	18	54541128	WDR7	Open sea	0.1024	0.01897	0.000000067	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg16400145	chr21:46359118	21	46359118	LINC01547;FAM207A	North shore	-0.0584	0.01083	0.000000068	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg25247351	chr6:32908794	6	32908794	HLA-DMB	Open sea	0.0714	0.01325	0.00000007	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg24886154	chr21:45138054	21	45138054	PDXK	North shore	-0.0383	0.00711	0.000000071	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg14369318	chr4:30759285	4	30759285	PCDH7	Open sea	0.0548	0.01018	0.000000072	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg12659626	chr11:2234975	11	2234975	-	Open sea	0.087	0.01616	0.000000072	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg06176777	chr21:39084502	21	39084502	KCNJ6	Open sea	-0.1407	0.02612	0.000000072	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg06883267	chr5:71813961	5	71813961	-	Open sea	0.0818	0.0152	0.000000072	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg03214130	chr7:36088642	7	36088642	-	Open sea	0.0541	0.01004	0.000000074	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg03237342	chr15:57425757	15	57425757	TCF12	Open sea	0.0954	0.01774	0.000000074	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg19442201	chr15:40572550	15	40572550	-	Island	-0.1752	0.03258	0.000000076	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg04524370	chr22:22292919	22	22292919	PPM1F	South shore	-0.046	0.00856	0.000000077	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg19635154	chr21:40326600	21	40326600	-	Open sea	-0.0497	0.00925	0.000000078	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg11750580	chr1:46088336	1	46088336	CCDC17	Island	-0.0959	0.01785	0.000000079	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg13953976	chr2:113542346	2	113542346	IL1A	Open sea	0.086	0.01601	0.00000008	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg02156899	chr16:2029256	16	2029256	NOXO1	Island	0.1211	0.02262	0.000000086	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg20619669	chr21:47659301	21	47659301	MCM3AP-AS1;MCM3AP	Open sea	-0.0362	0.00676	0.000000086	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg04467093	chr5:133448932	5	133448932	TCF7	North shore	0.0872	0.0163	0.000000089	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg13951450	chr9:99171316	9	99171316	ZNF367	Open sea	0.1168	0.02185	0.000000089	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg22004527	chr1:54638426	1	54638426	CYB5RL	Open sea	-0.0716	0.01339	0.000000089	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg04457572	chr10:73303234	10	73303234	CDH23	Open sea	0.0784	0.01467	0.00000009	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg23258940	chr19:55995851	19	55995851	NAT14;ZNF628	Island	0.0864	0.01621	0.0000001	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg11704631	chr21:36395663	21	36395663	RUNX1	North shelf	0.0707	0.0133	0.0000001	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg10207218	chr1:1714140	1	1714140	-	Island	-0.0591	0.01112	0.00000011	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg16826475	chr13:20749304	13	20749304	-	North shore	0.0946	0.01782	0.00000011	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg11646706	chr3:58514483	3	58514483	ACOX2	Open sea	0.1582	0.02975	0.00000011	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg19125089	chr21:44280344	21	44280344	WDR4	Open sea	-0.0405	0.00762	0.00000011	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg02748800	chr18:24229920	18	24229920	KCTD1	Open sea	0.0426	0.00802	0.00000011	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg17628249	chr17:58499854	17	58499854	C17orf64	South shore	0.0885	0.01672	0.00000012	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg13758712	chr21:28218959	21	28218959	ADAMTS1	South shore	-0.006	0.00113	0.00000012	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg25006435	chr1:154898438	1	154898438	PMVK	Open sea	-0.0508	0.00958	0.00000012	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg02231211	chr6:14459102	6	14459102	-	Open sea	0.0958	0.01808	0.00000012	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg04621850	chr9:140067121	9	140067121	TMEM210	North shore	0.0968	0.01826	0.00000012	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg01966117	chr3:52528714	3	52528714	STAB1	Open sea	-0.0641	0.01215	0.00000013	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg19414967	chr8:49468296	8	49468296	-	North shore	0.0821	0.01556	0.00000013	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg10619411	chr15:101514474	15	101514474	LRRK1	South shore	-0.1162	0.02199	0.00000013	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg08411860	chr3:183959746	3	183959746	VWA5B2	Island	0.0976	0.01859	0.00000015	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg24287218	chr6:33041268	6	33041268	HLA-DPA1	Open sea	0.064	0.01219	0.00000015	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg15504041	chr10:127477259	10	127477259	UROS	Open sea	-0.0378	0.0072	0.00000015	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg22563815	chr15:78856949	15	78856949	CHRNA5	North shore	-0.1038	0.01978	0.00000015	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg14790806	chr18:43858598	18	43858598	-	Open sea	-0.0371	0.00705	0.00000015	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg01230359	chr16:8728911	16	8728911	METTL22	Open sea	-0.0671	0.01278	0.00000015	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg26916625	chr21:46385436	21	46385436	FAM207A	North shore	-0.1121	0.02139	0.00000016	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg08350219	chr22:38627212	22	38627212	TMEM184B	Open sea	-0.0815	0.01555	0.00000016	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg16232270	chr3:67435396	3	67435396	SUCLG2	Open sea	-0.0806	0.01543	0.00000017	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg10167235	chr14:100807646	14	100807646	WARS	Open sea	0.0627	0.01202	0.00000018	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg14501219	chr17:62775713	17	62775713	LOC146880	Island	0.084	0.01609	0.00000018	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg23952057	chr19:1998686	19	1998686	BTBD2	North shore	-0.1394	0.02672	0.00000018	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg01026256	chr3:183959088	3	183959088	VWA5B2;MIR1224	Island	0.1841	0.03531	0.00000019	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg26275598	chr8:124167044	8	124167044	-	North shore	-0.07	0.01343	0.00000019	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg01808739	chr1:93912802	1	93912802	FNBP1L	North shore	0.1444	0.02779	0.0000002	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg17178761	chr17:55682851	17	55682851	MSI2	Open sea	0.1082	0.02082	0.0000002	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg23837804	chr21:45221122	21	45221122	RRP1	North shelf	0.0122	0.00234	0.0000002	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg00270625	chr22:51017019	22	51017019	CPT1B;CHKB-CPT1B	Island	0.2687	0.05173	0.0000002	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg16386697	chr22:51017162	22	51017162	CPT1B;CHKB-CPT1B	South shore	0.1684	0.03245	0.00000021	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg12226293	chr12:4333816	12	4333816	-	Open sea	0.0953	0.01838	0.00000021	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg13597043	chr1:90165225	1	90165225	LRRC8C	Open sea	0.0775	0.01496	0.00000022	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg00960204	chr6:140802228	6	140802228	-	Open sea	0.0863	0.01664	0.00000022	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg09655403	chr5:78985495	5	78985495	CMYA5	Open sea	-0.2626	0.05077	0.00000023	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg01062443	chr19:1609369	19	1609369	TCF3	South shelf	-0.0924	0.01787	0.00000023	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg23302438	chr1:155177953	1	155177953	MTX1;THBS3	North shore	0.0885	0.01709	0.00000023	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg19684059	chr21:47533179	21	47533179	COL6A2	South shore	-0.0709	0.01375	0.00000025	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg22530055	chr21:45373097	21	45373097	AGPAT3	Open sea	-0.0403	0.00782	0.00000025	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg16128973	chr15:42749836	15	42749836	ZNF106	Open sea	0.0854	0.01655	0.00000025	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg03429644	chr2:9252446	2	9252446	-	Open sea	0.1197	0.02326	0.00000026	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg07210082	chr2:20385524	2	20385524	-	Open sea	0.0912	0.0177	0.00000026	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg03938777	chr12:104439124	12	104439124	GLT8D2	Open sea	-0.0441	0.00856	0.00000026	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg12605353	chr8:55083464	8	55083464	-	Open sea	0.0768	0.0149	0.00000026	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg09983920	chr10:98898179	10	98898179	SLIT1	Open sea	-0.1014	0.01971	0.00000027	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg12711754	chr14:71247286	14	71247286	MAP3K9	Open sea	0.0692	0.01345	0.00000027	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg19546057	chr11:128776216	11	128776216	C11orf45;KCNJ5	Open sea	0.0836	0.01627	0.00000028	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg16674433	chr17:19314408	17	19314408	RNF112	Open sea	-0.1247	0.0243	0.00000028	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg26862744	chr21:27750466	21	27750466	-	Open sea	-0.0337	0.00655	0.00000028	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg19063680	chr21:31121244	21	31121244	GRIK1-AS1;GRIK1	Open sea	-0.0688	0.01339	0.00000028	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg13468961	chr2:172944338	2	172944338	MAP1D	North shore	-0.1245	0.02427	0.00000029	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg00927594	chr15:101514299	15	101514299	LRRK1	Island	-0.1544	0.03012	0.00000029	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg24473995	chr21:37539151	21	37539151	DOPEY2	Open sea	-0.0568	0.01107	0.00000029	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg15629519	chr2:13793275	2	13793275	-	Open sea	-0.1594	0.03105	0.00000029	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg09321817	chr6:33041343	6	33041343	HLA-DPA1	Open sea	0.0857	0.01673	0.0000003	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg24691814	chr1:65673302	1	65673302	AK4	Open sea	0.0676	0.01319	0.0000003	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg27588974	chr10:135164283	10	135164283	PRAP1	Open sea	0.0609	0.01189	0.00000031	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg19834377	chr12:12031125	12	12031125	ETV6;RNU6-19P	Open sea	0.0832	0.01629	0.00000032	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg27165960	chr5:39177381	5	39177381	FYB	Open sea	-0.0674	0.0132	0.00000033	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg24421519	chr21:34763007	21	34763007	-	Open sea	-0.0408	0.00799	0.00000033	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg03654166	chr2:172944393	2	172944393	MAP1D	North shore	-0.0958	0.01879	0.00000034	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg21615763	chr6:121843518	6	121843518	-	Open sea	0.1093	0.02145	0.00000034	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg00805292	chr8:49816427	8	49816427	-	Open sea	0.0937	0.01837	0.00000034	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg09195771	chr10:4312482	10	4312482	-	Open sea	0.0605	0.01187	0.00000034	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg22993195	chr3:49756301	3	49756301	AMIGO3;RNF123	Island	0.1475	0.02899	0.00000036	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg04659944	chr1:94684108	1	94684108	ARHGAP29	Open sea	-0.1353	0.02659	0.00000036	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg18464274	chr12:42537617	12	42537617	GXYLT1	North shore	0.0697	0.01372	0.00000037	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg18652327	chr13:94500648	13	94500648	GPC6	Open sea	0.1352	0.02658	0.00000037	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg10721284	chr8:10921222	8	10921222	XKR6	Open sea	0.0963	0.01894	0.00000037	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg02987388	chr1:46089045	1	46089045	CCDC17	Island	-0.1642	0.03232	0.00000038	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg14526825	chr21:46646076	21	46646076	ADARB1	Open sea	-0.0539	0.01062	0.00000038	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg00092301	chr5:142600451	5	142600451	ARHGAP26	Open sea	0.1266	0.02493	0.00000038	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg08811332	chr21:43185385	21	43185385	RIPK4	North shore	-0.0838	0.01654	0.0000004	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg26818573	chr2:46717839	2	46717839	-	Open sea	0.0815	0.01609	0.00000041	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg06546183	chr21:44257072	21	44257072	-	North shore	-0.0581	0.01148	0.00000041	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg00991639	chr8:110605574	8	110605574	SYBU	Open sea	0.0794	0.01572	0.00000044	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg14799482	chr1:90135931	1	90135931	LRRC8C	Open sea	0.1762	0.03492	0.00000045	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg12500589	chr21:41838303	21	41838303	DSCAM	Open sea	-0.0488	0.00969	0.00000047	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg18133309	chr17:72619827	17	72619827	CD300E	Open sea	0.0587	0.01165	0.00000047	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg18369748	chr7:43541717	7	43541717	HECW1	Open sea	0.0704	0.01401	0.0000005	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg08960443	chr9:140066947	9	140066947	TMEM210	North shore	0.122	0.02428	0.0000005	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg14980883	chr7:16835396	7	16835396	AGR2	Open sea	0.1309	0.02604	0.0000005	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg13003878	chr9:116840825	9	116840825	AMBP	Open sea	0.0792	0.01577	0.00000051	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg02910020	chr21:36883608	21	36883608	LOC100506403	Open sea	-0.0577	0.0115	0.00000051	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg23279355	chr5:78985592	5	78985592	CMYA5	Open sea	-0.1901	0.0379	0.00000052	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg05943655	chr6:43636172	6	43636172	RSPH9	Open sea	0.0474	0.00945	0.00000052	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg27141801	chr16:70366767	16	70366767	DDX19B;LOC100506083	Open sea	0.0477	0.00952	0.00000053	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg24425316	chr18:77400225	18	77400225	-	South shore	0.0704	0.01408	0.00000058	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg02185666	chr2:206549667	2	206549667	NRP2	Island	-0.0799	0.01601	0.0000006	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg04227885	chr17:2434802	17	2434802	-	Open sea	-0.1199	0.02403	0.0000006	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg24485927	chr2:795989	2	795989	-	Open sea	0.1163	0.02336	0.00000064	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg17967059	chr13:20763457	13	20763457	GJB2	North shelf	0.0538	0.01081	0.00000064	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg00253658	chr16:54210496	16	54210496	-	Open sea	0.279	0.05603	0.00000064	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg24768187	chr6:31646077	6	31646077	LY6G5C	North shelf	-0.0681	0.01368	0.00000065	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg04543319	chr20:30435686	20	30435686	-	North shore	0.0753	0.01515	0.00000066	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg02285386	chr22:35695157	22	35695157	TOM1	North shore	-0.028	0.00564	0.00000066	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg04168235	chr16:75282179	16	75282179	BCAR1	North shelf	-0.094	0.01893	0.00000067	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg14387452	chr9:20512334	9	20512334	MLLT3	Open sea	0.0635	0.01278	0.00000068	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg06571187	chr1:209878123	1	209878123	HSD11B1	Open sea	0.0723	0.01458	0.00000071	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg19871235	chr12:71552569	12	71552569	TSPAN8	Open sea	0.1512	0.0305	0.00000072	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg11731280	chr9:140066934	9	140066934	TMEM210	North shore	0.1069	0.02158	0.00000073	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg14008974	chr8:131012240	8	131012240	FAM49B	Open sea	0.0622	0.01257	0.00000073	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg10060399	chr16:725168	16	725168	RHBDL1	Open sea	0.0615	0.01243	0.00000074	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg21644387	chr2:663024	2	663024	-	South shelf	-0.06	0.01212	0.00000075	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg23198623	chr2:111433128	2	111433128	BUB1	North shelf	-0.0834	0.01686	0.00000075	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg23678254	chr14:55647471	14	55647471	DLGAP5	Open sea	-0.1439	0.02909	0.00000076	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg02626395	chr7:151615549	7	151615549	-	Open sea	0.0733	0.01483	0.00000076	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg11459843	chr2:223313524	2	223313524	SGPP2	Open sea	0.0812	0.01643	0.00000078	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg10537253	chr21:46542848	21	46542848	ADARB1	Open sea	-0.059	0.01193	0.00000078	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg12171807	chr20:61914812	20	61914812	ARFGAP1	North shore	-0.0541	0.01095	0.0000008	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg00502597	chr1:60197222	1	60197222	FGGY	Open sea	0.0557	0.01129	0.00000081	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg01804934	chr6:33041229	6	33041229	HLA-DPA1	Open sea	0.1211	0.02455	0.00000081	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg04259752	chr8:23262159	8	23262159	LOXL2	South shore	-0.0803	0.01628	0.00000081	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg04868991	chr15:101514483	15	101514483	LRRK1	South shore	-0.1511	0.03061	0.00000081	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg14025021	chr15:43809510	15	43809510	MAP1A	Open sea	0.0719	0.01459	0.00000084	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg26895804	chr8:145917243	8	145917243	-	Open sea	0.065	0.01323	0.00000088	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg07145284	chr11:66084631	11	66084631	CD248	South shore	0.0524	0.01066	0.00000088	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg14747819	chr16:65580692	16	65580692	LINC00922	Open sea	0.1239	0.0252	0.00000088	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg17595624	chr12:13246810	12	13246810	GSG1	Open sea	0.0704	0.01433	0.00000089	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg07332757	chr16:88593924	16	88593924	ZFPM1	South shelf	-0.0912	0.01856	0.0000009	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg05378523	chr11:128774371	11	128774371	C11orf45;KCNJ5	Open sea	-0.1789	0.03642	0.0000009	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg10333023	chr11:128774411	11	128774411	KCNJ5;C11orf45	Open sea	-0.1378	0.02805	0.00000091	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg23346329	chr1:90412171	1	90412171	-	Open sea	0.0521	0.01063	0.00000094	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg12843033	chr21:45706043	21	45706043	AIRE	Island	-0.0742	0.01514	0.00000096	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg24510074	chr7:128802865	7	128802865	TSPAN33	Open sea	-0.0785	0.01607	0.000001	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg16365373	chr10:102898409	10	102898409	-	North shore	0.1098	0.02254	0.0000011	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg06735127	chr12:124805929	12	124805929	-	North shelf	-0.0475	0.00974	0.0000011	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg25134852	chr2:71701721	2	71701721	DYSF	Open sea	0.0461	0.00946	0.0000011	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg00976623	chr14:69389034	14	69389034	ACTN1	Open sea	0.0553	0.01137	0.0000011	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg18411015	chr4:55650446	4	55650446	-	Open sea	0.0695	0.01425	0.0000011	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg25614875	chr1:217263847	1	217263847	ESRRG	South shore	0.14	0.02884	0.0000012	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg04154027	chr5:78985588	5	78985588	CMYA5	Open sea	-0.1954	0.0402	0.0000012	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg02068596	chr6:14068147	6	14068147	-	Open sea	-0.1543	0.03174	0.0000012	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg08827454	chr6:30922981	6	30922981	-	North shore	0.0554	0.01139	0.0000012	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg18017575	chr7:75213863	7	75213863	HIP1	Open sea	0.0754	0.01551	0.0000012	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg27292710	chr11:128772555	11	128772555	KCNJ5;C11orf45	Open sea	-0.0929	0.0192	0.0000013	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg25837377	chr9:37472460	9	37472460	-	Open sea	0.0766	0.01581	0.0000013	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg21350115	chr2:188312833	2	188312833	CALCRL	Open sea	0.0639	0.01324	0.0000014	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg03546977	chr5:78985489	5	78985489	CMYA5	Open sea	-0.1205	0.02503	0.0000015	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg02212173	chr1:243876835	1	243876835	AKT3	Open sea	0.0952	0.0198	0.0000015	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg07111846	chr21:43771349	21	43771349	TFF2	Open sea	-0.0371	0.00772	0.0000015	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg18878242	chr3:186848672	3	186848672	RPL39L	Open sea	0.1404	0.02917	0.0000015	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg07854108	chr21:27011836	21	27011836	JAM2	Island	-0.0043	0.00089	0.0000015	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg01585030	chr21:39811743	21	39811743	ERG	Open sea	-0.0506	0.01051	0.0000015	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg15197065	chr5:78985562	5	78985562	CMYA5	Open sea	-0.165	0.03438	0.0000016	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg25921609	chr17:8379225	17	8379225	MYH10	North shore	0.1315	0.02743	0.0000016	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg10257870	chr5:78985484	5	78985484	CMYA5	Open sea	-0.1726	0.03601	0.0000017	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg03940776	chr6:158490013	6	158490013	SYNJ2	Open sea	-0.0763	0.01592	0.0000017	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg24520862	chr11:75943228	11	75943228	-	North shelf	-0.0867	0.01813	0.0000017	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg15610027	chr18:32173227	18	32173227	DTNA	Open sea	0.1223	0.02555	0.0000017	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg17929770	chr19:46318514	19	46318514	RSPH6A	Island	0.0419	0.00875	0.0000017	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg18179663	chr20:36619159	20	36619159	TTI1	Open sea	-0.0534	0.01114	0.0000017	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg25116132	chr6:93750333	6	93750333	-	Open sea	0.029	0.00607	0.0000018	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg04790662	chr8:82005985	8	82005985	PAG1	Open sea	0.1788	0.03743	0.0000018	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg15728109	chr10:12375952	10	12375952	-	Open sea	0.0707	0.01483	0.0000018	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg03135912	chr21:47531289	21	47531289	COL6A2	North shore	-0.0212	0.00444	0.0000019	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg24632830	chr7:137402780	7	137402780	DGKI	Open sea	0.1367	0.02871	0.0000019	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg10981238	chr21:37674763	21	37674763	-	Open sea	-0.0472	0.00994	0.000002	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg09973676	chr8:82006417	8	82006417	PAG1	Open sea	0.2047	0.04312	0.0000021	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg26939946	chr17:19314395	17	19314395	RNF112	Open sea	-0.1167	0.02461	0.0000021	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg08805869	chr4:169632391	4	169632391	PALLD	Open sea	0.0615	0.01297	0.0000021	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg12205230	chr1:154164951	1	154164951	TPM3	Open sea	0.0389	0.00821	0.0000022	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg01819568	chr4:55528138	4	55528138	KIT	South shelf	0.0898	0.01898	0.0000022	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg25500267	chr8:55121968	8	55121968	-	Open sea	0.0768	0.01623	0.0000022	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg05096467	chr17:56744490	17	56744490	TEX14	Open sea	0.1078	0.02287	0.0000024	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg22697517	chr17:42785378	17	42785378	DBF4B	North shore	0.0372	0.0079	0.0000025	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg10127530	chr21:44732886	21	44732886	-	Open sea	-0.0648	0.01377	0.0000025	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg01290904	chr4:5708474	4	5708474	EVC2	North shore	0.0976	0.02077	0.0000026	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg10072328	chr15:95286906	15	95286906	-	Open sea	0.096	0.02042	0.0000026	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg22345137	chr10:73358422	10	73358422	CDH23	Open sea	0.0503	0.01072	0.0000026	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg14201617	chr2:47382452	2	47382452	C2orf61	Open sea	-0.0477	0.01015	0.0000027	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg15800404	chr21:37757105	21	37757105	CHAF1B	North shore	-0.0656	0.01398	0.0000027	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg10472537	chr2:105348800	2	105348800	-	Open sea	0.0756	0.01612	0.0000028	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg04086778	chr6:6002190	6	6002190	NRN1	North shore	0.0676	0.01448	0.000003	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg02773588	chr3:48698519	3	48698519	CELSR3	Island	0.1135	0.02434	0.0000031	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg16071713	chr21:36412456	21	36412456	C21orf96;RUNX1	Open sea	0.0396	0.00849	0.0000031	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg05381256	chr21:36089941	21	36089941	CLIC6	Open sea	-0.0361	0.00773	0.0000031	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg06261268	chr2:46689340	2	46689340	-	Open sea	0.0518	0.01111	0.0000032	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg15249796	chr17:56744413	17	56744413	TEX14	Open sea	0.1148	0.02467	0.0000033	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg24330456	chr6:30038955	6	30038955	RNF39	Island	0.0971	0.0209	0.0000034	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg21364696	chr1:36839798	1	36839798	STK40	Open sea	-0.0335	0.00724	0.0000037	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg15942325	chr8:9268401	8	9268401	-	Open sea	0.1014	0.02195	0.0000039	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg22470272	chr17:55631524	17	55631524	MSI2	Open sea	0.0566	0.01226	0.0000039	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg00958031	chr11:94259284	11	94259284	C11orf97	Open sea	0.0686	0.01487	0.000004	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg11213757	chr12:110511536	12	110511536	-	Open sea	0.0414	0.00899	0.0000042	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg11949606	chr21:34096277	21	34096277	SYNJ1	North shelf	-0.0344	0.00748	0.0000044	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg15285786	chr1:94559976	1	94559976	ABCA4	Open sea	0.05	0.01094	0.0000049	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg25073708	chr9:132083538	9	132083538	C9orf106	Island	0.0738	0.01617	0.000005	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg10742523	chr4:55650393	4	55650393	-	Open sea	0.0646	0.01417	0.0000051	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg07474825	chr19:10677826	19	10677826	KRI1;CDKN2D	North shore	-0.0451	0.00988	0.0000052	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg01121199	chr18:44626682	18	44626682	KATNAL2	Open sea	-0.0898	0.01972	0.0000053	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg24170424	chr11:8364582	11	8364582	-	Open sea	-0.0373	0.00821	0.0000054	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg26366371	chr1:245664079	1	245664079	KIF26B	Open sea	0.0666	0.01465	0.0000055	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg01071534	chr21:46385572	21	46385572	C21orf70	North shore	-0.0313	0.00689	0.0000057	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg04539934	chr3:41038791	3	41038791	-	Open sea	-0.0352	0.00775	0.0000057	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg21173328	chr3:11119246	3	11119246	-	Open sea	0.0501	0.01104	0.0000057	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg19859698	chr14:61822607	14	61822607	PRKCH	Open sea	0.0886	0.01956	0.0000059	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg03239861	chr10:108718158	10	108718158	SORCS1	Open sea	0.0914	0.02016	0.0000059	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg00621943	chr6:31646236	6	31646236	LY6G5C	North shelf	-0.0596	0.01318	0.0000063	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg10915554	chr9:73021673	9	73021673	KLF9	Open sea	0.102	0.02267	0.0000068	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg11067407	chr11:113599852	11	113599852	-	Open sea	0.0694	0.01544	0.0000069	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg19025685	chr1:54638490	1	54638490	CYB5RL	Open sea	-0.0461	0.01026	0.0000069	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg03944314	chr1:33827344	1	33827344	PHC2;LOC101929464	Open sea	-0.0469	0.01046	0.0000072	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg09879253	chr17:45935359	17	45935359	-	Open sea	0.0679	0.01519	0.0000078	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg03890268	chr8:123502572	8	123502572	LOC105375734	Open sea	-0.0311	0.00699	0.0000083	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg27592871	chr1:228585413	1	228585413	MIR6742;TRIM11	South shelf	-0.0455	0.01025	0.0000092	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg15946312	chr5:180646880	5	180646880	-	Island	0.119	0.02694	0.00001	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg05142212	chr13:33563153	13	33563153	-	Open sea	0.0672	0.01524	0.00001	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg05347456	chr16:89690262	16	89690262	DPEP1	Open sea	0.1614	0.03675	0.000011	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg02436969	chr5:171822592	5	171822592	SH3PXD2B	Open sea	-0.076	0.0173	0.000011	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg22424909	chr13:113639318	13	113639318	MCF2L	South shelf	0.0721	0.01643	0.000012	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg16847377	chr4:3370988	4	3370988	RGS12	North shelf	0.055	0.01259	0.000013	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg19161022	chr21:45344711	21	45344711	AGPAT3	Open sea	-0.0235	0.0054	0.000014	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg05804288	chr16:17332576	16	17332576	XYLT1	Open sea	0.0632	0.01455	0.000014	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg01385679	chr20:45033155	20	45033155	ELMO2	North shore	-0.0498	0.01152	0.000015	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg05376738	chr1:212923780	1	212923780	NSL1	Open sea	0.0538	0.01246	0.000016	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg22863298	chr1:9007541	1	9007541	CA6	Open sea	0.0348	0.00808	0.000017	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg12258307	chr21:32931935	21	32931935	TIAM1	Island	-0.0057	0.00133	0.000018	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg07239198	chr5:40808267	5	40808267	-	Open sea	-0.0644	0.01513	0.000021	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg06730285	chr5:139945107	5	139945107	APBB3;SLC35A4	South shore	-0.0451	0.01068	0.000024	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg06527213	chr15:86315211	15	86315211	KLHL25;MIR1276	South shelf	0.0507	0.01202	0.000025	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg02218324	chr19:46318439	19	46318439	RSPH6A	North shore	0.0666	0.01583	0.000026	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg02521050	chr21:45287110	21	45287110	AGPAT3	Open sea	-0.046	0.01096	0.000027	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg23945483	chr21:45265007	21	45265007	-	Open sea	-0.0366	0.00875	0.000028	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg21135948	chr21:34915592	21	34915592	GART;SON	Island	-0.0059	0.00142	0.00003	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg06598163	chr21:43965159	21	43965159	SLC37A1	Open sea	-0.0345	0.00827	0.000031	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg10023324	chr3:149780400	3	149780400	-	Open sea	0.0676	0.01649	0.000041	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg19672982	chr11:2715154	11	2715154	KCNQ1;KCNQ1OT1	Open sea	-0.0239	0.00584	0.000044	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg26642540	chr16:89010147	16	89010147	CBFA2T3	South shore	-0.0377	0.00925	0.000046	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg07741395	chr9:129254157	9	129254157	MVB12B	Open sea	-0.0264	0.00654	0.000054	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg16835843	chr21:45363997	21	45363997	AGPAT3	South shore	-0.0362	0.00916	0.000078	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed
Muskens I	California Biobank Program	33547282	2021-02-05	Downs Syndrome	EFO_0001064	individuals with GATA1 mutation removed	Supplementary Table 2	DNA methylation	Downs Syndrome	sex, batch effects, cell composition (reference based), ancestry (genomic PCs)	Beta Values	None	Illumina HumanMethylationEPIC	Whole Blood	None	605	1	Infants	Both	Admixed	cg11456334	chr21:33506516	21	33506516	NCRNA00159	Open sea	0.0082	0.00209	0.000097	None	33547282_Muskens-I_downs_syndrome_individuals_with_gata1_mutation_removed