Table 1.
NHGRI Catalog associations replicated by PheWAS
| PheWAS phenotype | Cases | Region | Nearest gene | SNP | Odds ratio (95% CI) | P-value | NHGRI Catalog disease(s) | |
|---|---|---|---|---|---|---|---|---|
| Autoimmune | Psoriasis | 327 | 6p21.33 | HLA-C | rs10484554 | 1.71 (1.41, 2.08) | 6.2E-08 | Psoriasis |
| 6p21.33 | HCP5 | rs2395029 | 2.38 (1.74, 3.26) | 2.0E-08 | Psoriasis | |||
| Rheumatoid arthritis | 398 | 6p21.32 | C6orf10 | rs6910071 | 1.50 (1.27, 1.76) | 1.5E-06 | Rheumatoid arthritis | |
| 6p21.32 | HLA-DRB1 | rs660895 | 1.56 (1.33, 1.84) | 6.7E-08 | Rheumatoid arthritis | |||
| Hypothyroidisma | 2,042 | 9q22.33 | FOXE1 | rs7850258 | 0.77 (0.71, 0.83) | 1.1E-11 | Hypothyroidism | |
| Hematologic | Iron metabolism disorder | 40 | 6p22.2 | SLC17A1 | rs17342717 | 6.84 (4.36, 10.7) | 5.3E-17 | Serum ferritin |
| 6p22.2 | HFE | rs1800562 | 12.3 (7.64, 19.7) | 3.4E-25 | Serum transferrin | |||
| 6p22.1 | HIST1H2BJ | rs13194491 | 7.80 (4.76, 12.8) | 3.8E-16 | Serum transferrin | |||
| Neoplastic | Melanoma | 268 | 16q24.3 | MC1R | rs4785763 | 1.52 (1.27, 1.81) | 2.8E-06 | Melanoma |
| Nonmelanoma skin cancer | 1,931 | 6p25.3 | EXOC2 | rs12210050 | 1.32 (1.20, 1.45) | 6.0E-09 | Basal cell carcinoma | |
| Prostate cancer | 848 | 8q24.21 | Intergenic | rs1447295b | 1.61 (1.34, 1.92) | 2.8E-07 | Prostate cancer | |
| Circulatory | Myocardial infarction | 1,382 | 9p21.3 | CDKN2BAS | rs4977574 | 1.28 (1.17, 1.40) | 4.0E-08 | Myocardial infarction |
| Coronary atherosclerosis | 3,499 | 9p21.3 | CDKN2BAS | rs4977574b | 1.26 (1.18, 1.34) | 1.0E-12 | Coronary heart disease | |
| Atrial fibrillation | 1,950 | 4q25 | Intergenic | rs2200733 | 1.52 (1.34, 1.72) | 1.5E-10 | Atrial fibrillation | |
| Endocrine/metabolic | Type 1 diabetes | 615 | 6p21.32 | HLA-DQB1 | rs2647044 | 1.42 (1.24, 1.61) | 2.0E-07 | Type 1 diabetes |
| Type 2 diabetes | 3,122 | 10q25.2 | TCF7L2 | rs7903146b | 1.31 (1.23, 1.40) | 8.3E-16 | Type 2 diabetes | |
| Hypercholesterolemia | 4,518 | 1p13.3 | CELSR2 | rs646776 | 0.77 (0.70, 0.85) | 1.0E-07 | LDL & total cholesterol | |
| 2p24.1 | APOB | rs693 | 0.78 (0.73, 0.85) | 7.4E-10 | LDL & total cholesterol | |||
| 19p13.2 | LDLR | rs6511720 | 0.74 (0.65, 0.84) | 2.5E-06 | LDL cholesterol | |||
| Hyperglyceridemia | 492 | 11q23.3 | APOA5 | rs12272004 | 2.24 (1.70, 2.95) | 7.2E-09 | Triglycerides | |
| 11q23.3 | ZNF259 | rs964184 | 2.22 (1.78, 2.75) | 5.8E-13 | Hypertriglyceridemia | |||
| Gout | 769 | 4p16.1 | SLC2A9 | rs16890979 | 0.67 (0.59, 0.78) | 5.1E-08 | Serum urate | |
| rs13129697b | 0.72 (0.63, 0.81) | 2.4E-07 | Gout, Serum urate | |||||
| 4p16.1 | Intergenic | rs4698036 | 0.68 (0.60, 0.79) | 7.8E-08 | Serum urate | |||
| 4q22.1 | ABCG2 | rs2231142 | 1.72 (1.48, 1.99) | 1.0E-12 | Serum urate | |||
| Hyperbilirubinemia | 46 | 2q37.1 | UGT1A1 | rs887829b | 33.8 (14.5, 78.5) | 3.2E-16 | Serum bilirubin | |
| 2q37.1 | HEATR7B1 | rs2361502 | 7.74 (4.72, 12.7) | 4.2E-16 | Serum bilirubin | |||
| Other | Alzheimer’s disease | 737 | 19q13.32 | TOMM40 | rs157580 | 0.70 (0.62, 0.80) | 8.6E-08 | Alzheimer’s disease |
| rs2075650 | 2.41 (2.06, 2.82) | 5.2E-28 | Alzheimer’s disease | |||||
| Age-related macular degeneration | 749 | 1q31.3 | CFH | rs1329428 | 0.51 (0.45, 0.59) | 7.2E-20 | Age-related macular degeneration | |
| 6p21.33 | SKIV2L/C2/CFB | rs429608 | 0.57 (0.46, 0.70) | 4.8E-08 | Age-related macular degeneration | |||
| Fuchs’ dystrophy | 108 | 18q21.2 | TCF4 | rs613872 | 2.61 (1.90, 3.58) | 2.9E-09 | Fuchs’ dystrophy |
Table limited to phenotypes that exceeded genome-wide significance in previously reported GWAS in individuals of European ancestry and that had a PheWAS P-value < 4.6 × 10−6 (FDR < 0.1). A comprehensive list of replication P-values, odds ratios, minor (reference) alleles and minor allele frequencies can be found in Supplementary Table 3.
a
This GWAS used a subset of this data set.
b
PheWAS results include other SNPs in LD with P < 4.6 × 10−6 (Supplementary Tables 3 and 8).