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. 2023 Jan 18;613(7944):508–518. doi: 10.1038/s41586-022-05473-8

Table 1.

A total of 30 previously unreported associations identified in a GWAS of 15 selected, previously extensively studied phenotypes

Phenotype rsID (hg38)a MAFFinnGen/ MAFNFSEE Protein change (HGVSp)b Function of variantc Gened Meta-analysis OR; P FinnGen AF %; OR; P EstBB AF %; OR; P UKBB AF %; OR; P
IBD rs748670681 115.0 Intron TNRC18 3.2; 2.4 × 10−61 3.6; 3.2; 1.1 × 10−56 1.3; 3.9; 2.8 × 10–06 NA; NA; NA
Ankylosing spondylitis rs748670681 115.0 Intron TNRC18 3.4; 3.6 × 10−31 3.6; 4.2; 1.8 × 10−34 1.3; 1.4; 0.11 NA; NA; NA
Type 2 diabetes rs45551238 9.6 5′ UTR ATP5E 0.8; 6.6 × 10−24 5.0; 0.8; 2.2 × 10−19 1.1; 0.7; 0.001 0.7; 0.8; 0.001
Primary open-angle glaucomae rs377027713 (rs147660927, PIP: 0.293) 87.4 p.Arg220Cys Upstream gene (missense) TARDBP (ANGPTL7) 0.7; 2.6 × 10−14 4.3; 0.6; 1.5 × 10−12 1.1; 0.7; 0.003 NA; NA; NA
Type 2 diabetes Chromosome 23: 56173773:A:C 3.6 Intergenic 1.1; 3.2 × 10−13 4.8; 1.1; 2.2 × 10−10 1.8; 1.2; 0.016 1.4; 1.1; 0.005
Atrial fibrillation rs190065070 (rs199600574, PIP:0.051) 16.6 p.Arg1845Trp Intergenic (missense) (MYH14) 1.4; 2.3 × 10−12 2.1; 1.4; 1.9 × 10−12 0.6; 1.2; 0.46 NA; NA; NA
Asthma rs74630264 (PIP: 0.232) 13.6 p.Ala82Thr Regulatory region (missense) (IL4R) 0.9; 1.1 × 10−11 8.2; 0.9; 2.5 × 10−12 2.9; 0.9; 0.061 0.7; 1; 0.72
Atrial fibrillation rs147972626 (PIP: 0.69) 2.7 p.Arg242Trp Missense RPL3L (RPL3L) 1.4; 1.1 × 10−11 1.3; 1.5; 8.2 × 10−11 0.64; 1.5; 0.033 0.6; 1.2; 0.017
Psoriasis rs138009430 (rs144651842, PIP: 0.211) 136.0 p.Ala82Thr Regulatory region (missense) FLJ21408 (IL4R) 1.2; 1.9 × 10−11 7.9; 1.3; 3.5 × 10−9 2.8; 1.2; 0.001 0.7; 1.1; 0.51
Myocardial infarction rs534125149 (PIP: 0.232) INFf p.Asn239dup Inframe insertion MFGE8 0.7; 3.8 × 10−11 2.9; 0.7; 1.1 × 10−10 0.6; 0.7; 0.14 NA; NA; NA
Atrial fibrillation rs201864074 (PIP: 0.536) 23.1 p.Arg4Gln Missense RPL3L 1.5; 9.2 × 10−11 1.2; 1.5; 1.4 × 10−8 0.27; 1.6; 0.1 0.04; 2.7; 0.001
Psoriasis rs748670681 115.0 Intron TNRC1 1.4; 1.2 × 10−10 3.6; 1.6; 1.2 × 10−13 1.3; 1.1; 0.27 NA; NA; NA
Breast cancer rs1457477682 0.9 Intergenic 1.1; 1.6 × 10−10 32; 1.1; 1.6 × 10−10 NA; NA; NA NA; NA; NA
Type 2 diabetes Chromosome 23: 48591031:T:C 1.5 Intron WDR13 0.9; 2.3 × 10−10 2.7; 0.9; 8.6 × 10−7 3.0; 0.9; 0.007 2.4; 0.9; 0.002
Type 2 diabetes rs190116876 57.7 Intron CTNNA3 1.3; 2.9 × 10−10 2.0; 1.4; 3.1 × 10−10 0.35; 1.2; 0.53 NA; NA; NA
Type 2 diabetes rs540205414 35.9 Upstream gene SCT 1.3; 3.1 × 10−10 1.4; 1.3; 2.1 × 10−9 0.74; 1.3; 0.048 NA; NA; NA
Type 2 diabetes rs1458770448(rs762966411, PIP: 0.141) INFf p.His293LeufsTer7 Intergenic (frameshift) (RFX6) 3.1; 5.2 × 10−10 0.1; 3.1; 5.2 × 10−10 NA; NA; NA NA; NA; NA
Atopic dermatitis rs2227472 0.9 Upstream gene IL22 1.1; 5.7 × 10−10 55.8; 1.1; 1.8 × 10−10 66.1; 0.66; 1; 0.07 59.3; 1.1; 0.004
Type 2 diabetes rs10835932 0.9 Intergenic 1.1; 7.7 × 10−9 18.4; 1.1; 7.2 × 10−7 18.7; 1.1; 0.023 20.2; 1; 0.009
Atrial fibrillation rs755287827 (rs766868752, PIP: 0.131) 9.4 c.105+1G>T Intron (splice donor) USP54 (SYNPO2L) 2.7; 9.6 × 10−9 0.14; 2.9; 3.2 × 10−9 0.057; 1.2; 0.71 NA; NA; NA
AMD rs139779213 (PIP: 0.467) INFf 3′ UTR CFI 2.1; 9.9 × 10−9 1.1; 2.0; 1.8 × 10−7 0.05; 6.8; 0.002 NA; NA; NA
Breast cancer rs1171552087 6.2 Intron CNTNAP2 33.1; 1.1 × 10−8 0.04; 33.1; 1.1 × 10−8 NA; NA; NA NA; NA; NA
Prostate cancer rs1301285839 INFf Downstream gene SNORA40 7.1; 1.2 × 10−8 0.1; 7.1; 1.2 × 10−8 NA; NA; NA NA; NA; NA
Atopic dermatitis rs950951813 (rs201208667, PIP: 0.191) INFf p.Cys379Tyr 3′ UTR (missense) SERPINB8 (SERPINB7) 1.6; 1.4 × 10−8 0.6; 2.1; 5.6 × 10−9 0.4; 1.3; 0.021 NA; NA; NA
Type 2 diabetes rs193302380 13.9 Intron SPATS2 1.1; 1.8 × 10−8 6.1; 1.1; 1.7 × 10−7 4.2; 1.1; 0.028 0.2; 1; 0.91
Asthma rs552196550 INFf Intron DYNC1I1 2.0; 2.3 × 10−8 0.3; 2.0; 2.3 × 10−8 NA; NA; NA NA; NA; NA
Prostate cancer rs954957419 (rs965427251, PIP: 0.44) 0.2 p.Ala139_Leu148del Intron (inframe deletion) TTLL1 (BIK) 3.5; 2.5 × 10−8 0.3; 3.5; 5.4 × 10−8 0.09; 3; 0.21 NA; NA; NA
Seropositive rheumatoid arthritis rs555210673 INFf Intron SFRP4 1.5; 2.7 × 10−8 2.3l 1.5; 7.4 × 10−7 0.4; 2.7; 0.002 NA; NA; NA
Primary open-angle glaucoma rs10658374 1.5 Upstream gene PAM 135.6; 2.7 × 10−8 0.03; 135.6; 2.7 × 10−8 NA; NA; NA NA; NA; NA
Atopic dermatitis rs775241954 INFf Intron NOTCH2 1.9; 3.8 × 10−8 0.6; 2.1; 2.7 × 10−8 0.2; 1.4; 0.16 NA; NA; NA

Table is ordered by meta-analysis P values in descending order of significance. All reported variants were mapped to GRCh38. Rows that are in bold are variants surpassing Bonferroni multiple testing correction for 15 end points (P < 3.3 × 10–9). NA, not applicable; UTR, untranslated region.

aThe coding variant rsID in PIP is given in parentheses if a coding variant was observed in the credible set (omitted if the reported lead variant was a coding variant).

bHGVS notation protein coding change is provided if either the lead variant was coding or coding credible was observed in the credible set (if either one exists).

cCoding variant consequence is given in parentheses in cases in which the lead variant was not a coding variant and a coding variant was observed in the credible set.

dGene corresponding to the variant function. In cases in which a lead variant was not a coding variant, but there was a coding variant in the credible set, the credible set coding variant gene is given in parentheses.

eWe have previously published the ANGPTL7 variant association with glaucoma35.

fDenotes values of infinity (INF) resulting from MAFNFSEEbeing 0.00.