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 Battram T GEO 30602389 2020-09-15 Tissue None EWAS Catalog re-analysis of GEO data. GEO accession ID is GSE124366. Tissue types are buccal epithelial cells and peripheral blood mononuclear cells None DNA methylation Tissue Batch effects, cell composition (reference free) Beta Values None Illumina HumanMethylation450 Buccal cells and peripheral blood mononuclear cells None 215 1 Children Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.27537 0.00685 1e-95 None 30602389_Battram-T_tissue_ewas_catalog_re-analysis_of_geo_data__geo_accession_id_is_gse124366__tissue_types_are_buccal_epithelial_cells_and_peripheral_blood_mononuclear_cells Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P02748 None OSCA model 1 10.5281/zenodo.16924748 DNA methylation P02748 Age,Sex M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.123379 0.00819349 7.312910999999999e-51 P02748 41361833_Josephine_Robertson_P02748_OSCA_model_1 Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P18428 None OSCA model 1 10.5281/zenodo.16924748 DNA methylation P18428 Age,Sex M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.109644 0.00820679 1.783059e-40 P18428 41361833_Josephine_Robertson_P18428_OSCA_model_1 Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P02750 None OSCA model 1 10.5281/zenodo.16924748 DNA methylation P02750 Age,Sex M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.109613 0.00820682 1.874835e-40 P02750 41361833_Josephine_Robertson_P02750_OSCA_model_1 Bonder MJ - 25282492 2014-10-04 Fetal vs adult liver UBERON_0002107, GO_0048513 - Additional file 2 DNA methylation Fetal vs adult liver Sex and technical covariates M values - Illumina HumanMethylation450 Liver - 195 2 - Missing None cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -2.69348 0.11368 1.04e-39 - 25282492_fetal_vs_adult_liver Yao C FHS, KORA F4, BLSA, InCHIANTI 33752734 2021-03-22 Gene expression of Affymetrix ID: 2451155 (gene symbol: PTPN7) None Meta-analysis Table S6 DNA methylation Gene expression of Affymetrix ID: 2451155 (gene symbol: PTPN7) Age, sex, cell composition (reference based), batch effects Beta Values None Illumina HumanMethylation450 Whole blood None 4170 1 Adults Both Unclear cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea None None 8.100000000000001e-37 None 33752734_Yao-C_gene_expression_of_affymetrix_id__2451155__gene_symbol__ptpn7__meta-analysis Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P01742 None OSCA model 1 10.5281/zenodo.16924748 DNA methylation P01742 Age,Sex M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.0866837 0.00822549 7.108397e-26 P01742 41361833_Josephine_Robertson_P01742_OSCA_model_1 Robert F Hillary Generation Scotland 10.1101/2023.01.10.23284387 9/6/2023 Incident COPD None Basic model https://doi.org/10.5281/zenodo.8021411 DNA methylation Incident COPD Age, Sex, Cell composition (reference based) M values None Illumina HumanMethylationEPIC Whole blood None 17902 1 Adults (18-65y) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.043 0.00458 2.5e-21 None Robert-F-Hillary_Incident_COPD_Basic_model Marttila S - 25888029 2015-03-14 Ageing GO_0007568 - Additional file 1 DNA methylation Age group Sex and cell counts Beta values - Illumina HumanMethylation450 Peripheral blood mononuclear cells Variable dispersion beta regression model 143 1 58.5 Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.98294 0.1043 4.4900000000000005e-21 - 25888029_ageing Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P06396 None OSCA model 1 10.5281/zenodo.16924748 DNA methylation P06396 Age,Sex M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea 0.0744421 0.00823366 1.7406879999999998e-19 P06396 41361833_Josephine_Robertson_P06396_OSCA_model_1 Hannah M. Smith Generation Scotland 39706196 Jan 2, 2025 BMI EFO_0004340 discovery None DNA methylation BMI Age,Sex,Smoking,Cell composition (reference based),Batch effects Other kg/m2 Illumina HumanMethylationEPIC Whole blood None 17304 1 Adults Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.239929 0.026763 3.414719e-19 None 39706196_Hannah-M.-Smith_bmi_discovery Hannah M. Smith Generation Scotland 39706196 Jan 2, 2025 Waist-hip ratio EFO_0004343 discovery None DNA methylation Waist-hip ratio Age,Sex,Smoking,Cell composition (reference based),Batch effects Other None Illumina HumanMethylationEPIC Whole blood None 17304 1 Adults Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.221138 0.0267515 1.47966e-16 None 39706196_Hannah-M.-Smith_waist-hip_ratio_discovery Robert F. Hillary Generation Scotland doi.org/10.1101/2023.11.02.23298000 Nov 3, 2023 C-reactive protein (CRP) levels None Basic model None C-reactive protein (CRP) levels DNA methylation Age, Sex, Cell composition (reference based), Batch effects mg/L Beta values Illumina HumanMethylationEPIC Whole blood None 17936 1 Adults Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -2.2 0.276 5e-16 Basic_Model Robert-F.-Hillary_c-reactive_protein__crp__levels_basic_model Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P04114 None OSCA model 1 10.5281/zenodo.16924748 DNA methylation P04114 Age,Sex M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea 0.0651426 0.00823903 0.000000000000002833168 P04114 41361833_Josephine_Robertson_P04114_OSCA_model_1 Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P27169 None OSCA model 1 10.5281/zenodo.16924748 DNA methylation P27169 Age,Sex M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea 0.0635129 0.0082399 0.00000000000001360128 P27169 41361833_Josephine_Robertson_P27169_OSCA_model_1 Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 A0A0G2JMB2 None OSCA model 2 10.5281/zenodo.16924748 DNA methylation A0A0G2JMB2 Age,Sex,Cell composition (reference based) M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.0776864 0.0101603 0.00000000000002200895 A0A0G2JMB2 41361833_Josephine_Robertson_A0A0G2JMB2_OSCA_model_2 Hannah M. Smith Generation Scotland 39706196 Jan 2, 2025 Body fat EFO_0007800 discovery None DNA methylation Body fat Age,Sex,Smoking,Cell composition (reference based),Batch effects Other % Illumina HumanMethylationEPIC Whole blood None 17304 1 Adults Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.203487 0.026842 0.00000000000003604714 None 39706196_Hannah-M.-Smith_body_fat_discovery Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P29622 None OSCA model 1 10.5281/zenodo.16924748 DNA methylation P29622 Age,Sex M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea 0.0610055 0.00824119 0.0000000000001408914 P29622 41361833_Josephine_Robertson_P29622_OSCA_model_1 Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P02671 None OSCA model 1 10.5281/zenodo.16924748 DNA methylation P02671 Age,Sex M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.0573336 0.00824299 0.000000000003663461 P02671 41361833_Josephine_Robertson_P02671_OSCA_model_1 Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P00740 None OSCA model 1 10.5281/zenodo.16924748 DNA methylation P00740 Age,Sex M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.057112 0.00824309 0.00000000000443137 P00740 41361833_Josephine_Robertson_P00740_OSCA_model_1 Hannah M. Smith Generation Scotland 39706196 Jan 2, 2025 HDL cholesterol EFO_0004612 discovery None DNA methylation HDL cholesterol Age,Sex,Smoking,Cell composition (reference based),Batch effects Other mmol/L Illumina HumanMethylationEPIC Whole blood None 18225 1 Adults Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea 0.178968 0.0261197 0.000000000007523119 None 39706196_Hannah-M.-Smith_hdl_cholesterol_discovery Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P00734 None OSCA model 1 10.5281/zenodo.16924748 DNA methylation P00734 Age,Sex M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea 0.0560246 0.0082436 0.00000000001116068 P00734 41361833_Josephine_Robertson_P00734_OSCA_model_1 Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P06396 None OSCA model 2 10.5281/zenodo.16924748 DNA methylation P06396 Age,Sex,Cell composition (reference based) M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea 0.0685144 0.0101494 0.00000000001527879 P06396 41361833_Josephine_Robertson_P06396_OSCA_model_2 Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 A0A0G2JMB2 None OSCA model 3 10.5281/zenodo.16924748 DNA methylation A0A0G2JMB2 Age,Sex,Cell composition (reference based),Body mass index, Smoking M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.0668235 0.010163 0.00000000005023042 A0A0G2JMB2 41361833_Josephine_Robertson_A0A0G2JMB2_OSCA_model_3 Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P01742 None OSCA model 2 10.5281/zenodo.16924748 DNA methylation P01742 Age,Sex,Cell composition (reference based) M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.0662438 0.0101064 0.00000000005762853 P01742 41361833_Josephine_Robertson_P01742_OSCA_model_2 Bohlin J - 27717397 2016-10-07 Gestational age EFO_0005112 Last menstrual period-estimated gestational age Table S2 DNA methylation Gestational age Offspring sex, maternal age, maternal smoking, study design, caesarean section and cell counts Beta values days Illumina HumanMethylation450 Cord blood - 1068 1 0 Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.00101954 0.00015496 0.0000000000739 - 27717397_gestational_age_last_menstrual_periodestimated_gestational_age Robert F Hillary Generation Scotland 10.1101/2023.01.10.23284387 9/6/2023 Incident Type 2 Diabetes None Basic model https://doi.org/10.5281/zenodo.8021411 DNA methylation Incident Type 2 Diabetes Age, Sex, Cell composition (reference based) M values None Illumina HumanMethylationEPIC Whole blood None 17749 1 Adults (18-65y) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.035 0.00539 0.000000000082 None Robert-F-Hillary_Incident_Type_2_Diabetes_Basic_model Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P04004 None OSCA model 1 10.5281/zenodo.16924748 DNA methylation P04004 Age,Sex M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.0529745 0.00824498 0.0000000001358849 P04004 41361833_Josephine_Robertson_P04004_OSCA_model_1 Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P18428 None OSCA model 2 10.5281/zenodo.16924748 DNA methylation P18428 Age,Sex,Cell composition (reference based) M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.0637042 0.0100589 0.0000000002472874 P18428 41361833_Josephine_Robertson_P18428_OSCA_model_2 Mulder RH ALSPAC,Generation R 33450751 25/01/2021 age EFO_0000246 Model 2 at 6y with age as a fixed effect http://epidelta.mrcieu.ac.uk/ DNA methylation age sex,gestational age,cohort,cell composition (reference based),batch effects Beta Values years Illumina HumanMethylation450 Whole blood None 2338 2 Children Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.0087 0.0014 0.00000000054 None 33450751_Mulder-RH_age_model_2_at_6y_with_age_as_a_fixed_effect Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P02647 None OSCA model 1 10.5281/zenodo.16924748 DNA methylation P02647 Age,Sex M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea 0.0496417 0.00824639 0.000000001787932 P02647 41361833_Josephine_Robertson_P02647_OSCA_model_1 Robert F Hillary Generation Scotland 10.1101/2023.01.10.23284387 9/6/2023 Prevalent Type 2 Diabetes (Self-report) None Basic model https://doi.org/10.5281/zenodo.8021411 DNA methylation Prevalent Type 2 Diabetes (Self-report) Age, Sex, Cell composition (reference based) M values None Illumina HumanMethylationEPIC Whole blood None 18005 1 Adults (18-65y) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.072 0.012 0.000000002 None Robert-F-Hillary_Prevalent_Type_2_Diabetes_(Self-report)_Basic_model Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P04275 None OSCA model 1 10.5281/zenodo.16924748 DNA methylation P04275 Age,Sex M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.0492086 0.00824657 0.000000002469718 P04275 41361833_Josephine_Robertson_P04275_OSCA_model_1 Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P02763 None OSCA model 1 10.5281/zenodo.16924748 DNA methylation P02763 Age,Sex M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.0477284 0.00824716 0.000000007300677 P02763 41361833_Josephine_Robertson_P02763_OSCA_model_1 Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P04003 None OSCA model 1 10.5281/zenodo.16924748 DNA methylation P04003 Age,Sex M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea 0.0476229 0.0082472 0.000000007877649 P04003 41361833_Josephine_Robertson_P04003_OSCA_model_1 Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P01008 None OSCA model 1 10.5281/zenodo.16924748 DNA methylation P01008 Age,Sex M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea 0.0471372 0.00824739 0.00000001115673 P01008 41361833_Josephine_Robertson_P01008_OSCA_model_1 Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P08185 None OSCA model 1 10.5281/zenodo.16924748 DNA methylation P08185 Age,Sex M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea 0.0467359 0.00824755 0.00000001483582 P08185 41361833_Josephine_Robertson_P08185_OSCA_model_1 Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P02647 None OSCA model 2 10.5281/zenodo.16924748 DNA methylation P02647 Age,Sex,Cell composition (reference based) M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea 0.0568648 0.0101292 0.0000000201379 P02647 41361833_Josephine_Robertson_P02647_OSCA_model_2 Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P00450 None OSCA model 1 10.5281/zenodo.16924748 DNA methylation P00450 Age,Sex M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.0450897 0.00824817 0.00000004661823 P00450 41361833_Josephine_Robertson_P00450_OSCA_model_1 Robert F Hillary Generation Scotland 10.1101/2023.01.10.23284387 9/6/2023 Prevalent COPD (Self-report) None Basic model https://doi.org/10.5281/zenodo.8021411 DNA methylation Prevalent COPD (Self-report) Age, Sex, Cell composition (reference based) M values None Illumina HumanMethylationEPIC Whole blood None 18078 1 Adults (18-65y) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.044 0.00804 0.000000047 None Robert-F-Hillary_Prevalent_COPD_(Self-report)_Basic_model Li S - 28811542 2017-08-15 Age EFO_0000246 - Table S1 DNA methylation Age Cell counts M values years Illumina HumanMethylation450 Whole blood - 1366 2 73 Missing European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.0112 0.00211181 0.0000000568 - 28811542_age Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 A0A075B6I1 None OSCA model 1 10.5281/zenodo.16924748 DNA methylation A0A075B6I1 Age,Sex M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.0446231 0.00824835 0.00000006403409 A0A075B6I1 41361833_Josephine_Robertson_A0A075B6I1_OSCA_model_1 Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P06396 None OSCA model 3 10.5281/zenodo.16924748 DNA methylation P06396 Age,Sex,Cell composition (reference based),Body mass index, Smoking M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea 0.0540923 0.0101135 0.00000009000202 P06396 41361833_Josephine_Robertson_P06396_OSCA_model_3 Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 B1AHL2 None OSCA model 2 10.5281/zenodo.16924748 DNA methylation B1AHL2 Age,Sex,Cell composition (reference based) M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea 0.0531736 0.0101527 0.0000001651329 B1AHL2 41361833_Josephine_Robertson_B1AHL2_OSCA_model_2 Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P01031 None OSCA model 1 10.5281/zenodo.16924748 DNA methylation P01031 Age,Sex M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.0414134 0.00824949 0.0000005224674 P01031 41361833_Josephine_Robertson_P01031_OSCA_model_1 Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P01042 None OSCA model 1 10.5281/zenodo.16924748 DNA methylation P01042 Age,Sex M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea 0.0413636 0.00824951 0.0000005391158 P01042 41361833_Josephine_Robertson_P01042_OSCA_model_1 Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P06727 None OSCA model 1 10.5281/zenodo.16924748 DNA methylation P06727 Age,Sex M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea 0.04121 0.00824956 0.0000005938373 P06727 41361833_Josephine_Robertson_P06727_OSCA_model_1 Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P02790 None OSCA model 1 10.5281/zenodo.16924748 DNA methylation P02790 Age,Sex M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.0411486 0.00824958 0.0000006171866 P02790 41361833_Josephine_Robertson_P02790_OSCA_model_1 Hannah M. Smith Generation Scotland 39706196 Jan 2, 2025 Total cholesterol EFO_0004574 sensitivity None DNA methylation Total cholesterol Age,Sex,Smoking,Cell composition (reference based),Batch effects Other mmol/L Illumina HumanMethylationEPIC Whole blood None 18270 1 Adults Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea 0.202754 0.0408613 0.0000007039964 None 39706196_Hannah-M.-Smith_total_cholesterol_sensitivity Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P02649 None OSCA model 1 10.5281/zenodo.16924748 DNA methylation P02649 Age,Sex M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea 0.0400988 0.00824993 0.000001182971 P02649 41361833_Josephine_Robertson_P02649_OSCA_model_1 Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P00740 None OSCA model 2 10.5281/zenodo.16924748 DNA methylation P00740 Age,Sex,Cell composition (reference based) M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.0492054 0.0101503 0.000001262027 P00740 41361833_Josephine_Robertson_P00740_OSCA_model_2 Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P18428 None OSCA model 3 10.5281/zenodo.16924748 DNA methylation P18428 Age,Sex,Cell composition (reference based),Body mass index, Smoking M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.047948 0.00991959 0.000001353966 P18428 41361833_Josephine_Robertson_P18428_OSCA_model_3 Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P27169 None OSCA model 2 10.5281/zenodo.16924748 DNA methylation P27169 Age,Sex,Cell composition (reference based) M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea 0.0489159 0.0101492 0.000001452353 P27169 41361833_Josephine_Robertson_P27169_OSCA_model_2 Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P51884 None OSCA model 1 10.5281/zenodo.16924748 DNA methylation P51884 Age,Sex M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea 0.0396362 0.00825008 0.000001568006 P51884 41361833_Josephine_Robertson_P51884_OSCA_model_1 Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P01718 None OSCA model 1 10.5281/zenodo.16924748 DNA methylation P01718 Age,Sex M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.0394239 0.00825015 0.000001782572 P01718 41361833_Josephine_Robertson_P01718_OSCA_model_1 Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P02748 None OSCA model 2 10.5281/zenodo.16924748 DNA methylation P02748 Age,Sex,Cell composition (reference based) M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.0475409 0.00998136 0.000001925944 P02748 41361833_Josephine_Robertson_P02748_OSCA_model_2 Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 O75882 None OSCA model 1 10.5281/zenodo.16924748 DNA methylation O75882 Age,Sex M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea 0.0388864 0.00825033 0.00000245956 O75882 41361833_Josephine_Robertson_O75882_OSCA_model_1 Sikdar S CHARGE 31536415 2019-09-19 Smoking EFO_0009115, EFO_0006527, EFO_0004318 random effects meta-analysis Table S2 DNA methylation Smoking Age, sex, cell composition (reference based), batch effects Beta Values None Illumina HumanMethylation450 Whole blood, CD4+ T cells, CD14+ monocytes None 15907 16 Adults Both European, African, Other cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.00458 0.00097 0.0000025 None 31536415_Sikdar-S_smoking_random_effects_meta-analysis Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P01742 None OSCA model 3 10.5281/zenodo.16924748 DNA methylation P01742 Age,Sex,Cell composition (reference based),Body mass index, Smoking M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.0467287 0.00999976 0.00000299497 P01742 41361833_Josephine_Robertson_P01742_OSCA_model_3 Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 A0A0G2JMB2 None OSCA model 1 10.5281/zenodo.16924748 DNA methylation A0A0G2JMB2 Age,Sex M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.0384403 0.00825047 0.000003202898 A0A0G2JMB2 41361833_Josephine_Robertson_A0A0G2JMB2_OSCA_model_1 Kashima K None 33564054 2021-02-09 gestational age EFO_0005112 None Supplementary Table 6 DNA methylation gestational age sex, batch effects, cell composition (reference based), cesarean section, maternal pre-pregnancy bmi, maternal smoking before pregnancy, chorioamnionitis, idiopathic premature rupture of the membrane, preeclampsia Beta Values weeks Illumina HumanMethylation450 Cord blood None 110 1 Infants Both East Asian cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea 0.0037 0.00077 0.0000038 None 33564054_Kashima-K_gestational_age Robert F Hillary Generation Scotland 10.1101/2023.01.10.23284387 9/6/2023 Incident Ischemic Heart Disease None Basic model https://doi.org/10.5281/zenodo.8021411 DNA methylation Incident Ischemic Heart Disease Age, Sex, Cell composition (reference based) M values None Illumina HumanMethylationEPIC Whole blood None 17483 1 Adults (18-65y) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.024 0.00521 0.0000039 None Robert-F-Hillary_Incident_Ischemic_Heart_Disease_Basic_model Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P02751 None OSCA model 1 10.5281/zenodo.16924748 DNA methylation P02751 Age,Sex M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea 0.0361767 0.00825117 0.00001170976 P02751 41361833_Josephine_Robertson_P02751_OSCA_model_1 Dugue P-A Melbourne Collaborative Cohort Study 31789449 2019-11-04 Alcohol consumption EFO_0004329, EFO_0007878 Previous week consumption discovery Supplementary Table 3 Alcohol consumption DNA methylation age, sex, smoking, body mass index country of birth, sample type, cell composition (reference based), batch effects g/day M Values Illumina HumanMethylation450 Whole blood None 5606 1 Adults Both Unclear cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea None None 0.000013 None 31789449_Dugue-P-A_alcohol_consumption_previous_week_consumption_discovery Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P55056 None OSCA model 1 10.5281/zenodo.16924748 DNA methylation P55056 Age,Sex M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea 0.0356295 0.00825133 0.00001584636 P55056 41361833_Josephine_Robertson_P55056_OSCA_model_1 Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P04004 None OSCA model 2 10.5281/zenodo.16924748 DNA methylation P04004 Age,Sex,Cell composition (reference based) M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.0435918 0.0101415 0.00001731865 P04004 41361833_Josephine_Robertson_P04004_OSCA_model_2 Gadd DA Generation Scotland 35945220 31/07/2022 TNFRSF17 protein levels (SeqId = 2665-26) None SomaScan protein measurement https://doi.org/10.5281/zenodo.6801458 TNFRSF17 protein levels (SeqId = 2665-26) DNA methylation Age, sex, pQTLs, batch effects, ancestry (genomic PCs), depression, cell composition (reference based), body mass index, smoking None M values Illumina HumanMethylationEPIC Whole blood Full UniProt name: Tumor necrosis factor receptor superfamily member 17 774 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.52 0.123 0.000027 None Gadd-DA_tnfrsf17_protein_levels__seqid___2665-26__somascan_protein_measurement Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P08571 None OSCA model 1 10.5281/zenodo.16924748 DNA methylation P08571 Age,Sex M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.0345164 0.00825165 0.00002893998 P08571 41361833_Josephine_Robertson_P08571_OSCA_model_1 Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P01762 None OSCA model 1 10.5281/zenodo.16924748 DNA methylation P01762 Age,Sex M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.0341923 0.00825174 0.00003437512 P01762 41361833_Josephine_Robertson_P01762_OSCA_model_1 Gross AM - 27105112 2016-04-21 HIV infection EFO_0000764 CD4+ T-cells Table S2 DNA methylation HIV infection Age - - Illumina HumanMethylation450 CD4+ T-cells - 60 1 46.5 Males European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.479438 0.1181 0.0000493 None 27105112_hiv_infection_cd4_tcells Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P02748 None OSCA model 3 10.5281/zenodo.16924748 DNA methylation P02748 Age,Sex,Cell composition (reference based),Body mass index, Smoking M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.0405099 0.0100131 0.00005243578 P02748 41361833_Josephine_Robertson_P02748_OSCA_model_3 Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 B1AHL2 None OSCA model 3 10.5281/zenodo.16924748 DNA methylation B1AHL2 Age,Sex,Cell composition (reference based),Body mass index, Smoking M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea 0.0406405 0.010132 0.00006073788 B1AHL2 41361833_Josephine_Robertson_B1AHL2_OSCA_model_3 Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P27169 None OSCA model 3 10.5281/zenodo.16924748 DNA methylation P27169 Age,Sex,Cell composition (reference based),Body mass index, Smoking M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea 0.040425 0.0101479 0.00006820916 P27169 41361833_Josephine_Robertson_P27169_OSCA_model_3 Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P01023 None OSCA model 4 10.5281/zenodo.16924748 DNA methylation P01023 Age,Sex,Cell composition (reference based),Body mass index, Smoking,20 DNAm PCs M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.0678214 0.0170622 0.00007073231 P01023 41361833_Josephine_Robertson_P01023_OSCA_model_4 Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P05160 None OSCA model 1 10.5281/zenodo.16924748 DNA methylation P05160 Age,Sex M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea 0.0326347 0.00825217 0.00007699705 P05160 41361833_Josephine_Robertson_P05160_OSCA_model_1 Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P01718 None OSCA model 3 10.5281/zenodo.16924748 DNA methylation P01718 Age,Sex,Cell composition (reference based),Body mass index, Smoking M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.0401631 0.010209 0.00008390441 P01718 41361833_Josephine_Robertson_P01718_OSCA_model_3 Robert F Hillary Generation Scotland 10.1101/2023.01.10.23284387 9/6/2023 Prevalent Colorectal Cancer (Self-report) None Basic model https://doi.org/10.5281/zenodo.8021411 DNA methylation Prevalent Colorectal Cancer (Self-report) Age, Sex, Cell composition (reference based) M values None Illumina HumanMethylationEPIC Whole blood None 18055 1 Adults (18-65y) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.024 0.00602 0.000087 None Robert-F-Hillary_Prevalent_Colorectal_Cancer_(Self-report)_Basic_model Robert F Hillary Generation Scotland 10.1101/2023.01.10.23284387 9/6/2023 Prevalent Type 2 Diabetes (Self-report) None Fully-adjusted model https://doi.org/10.5281/zenodo.8021411 DNA methylation Prevalent Type 2 Diabetes (Self-report) Age, Sex, Cell composition (reference based), Ancestry (genomic PCs), Body mass index, Socio-economic position, Education, Alcohol consumption M values None Illumina HumanMethylationEPIC Whole blood None 14350 1 Adults (18-65y) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.05 0.0129 0.000097 None Robert-F-Hillary_Prevalent_Type_2_Diabetes_(Self-report)_Fully-adjusted_model Josephine Robertson Generation Scotland 41361833 Dec 8, 2025 P10643 None OSCA model 1 10.5281/zenodo.16924748 DNA methylation P10643 Age,Sex M values None Illumina HumanMethylationEPIC whole blood None 14671 1 Adults (18-65 years) Both European cg01437204 chr1:202130344 1 202130344 PTPN7 Open sea -0.0321601 0.0082523 0.00009778163 P10643 41361833_Josephine_Robertson_P10643_OSCA_model_1