Table 2.
Potentially novel associations discovered via PheWAS
| PheWAS phenotype | Cases | Region | Nearest gene | SNP | Odds ratio (95% CI) | P-value | NHGRI catalog disease(s) |
|---|---|---|---|---|---|---|---|
| Actinic keratosis | 2,505 | 5p13.2 | SLC45A2 | rs16891982 | 0.55 (0.44, 0.70) | 6.3E-07 | Hair, eye color, skin pigmentation |
| 6p25.3 | IRF4 | rs12203592 | 1.69 (1.53, 1.86) | 4.1E-26 | Hair, eye color, freckling, PSP | ||
| 6p25.3 | EXOC2 | rs12210050 | 1.32 (1.20, 1.45) | 1.9E-08 | Basal cell carcinoma, tanning | ||
| 15q13.1 | HERC2 | rs12913832 | 0.80 (0.73, 0.87) | 8.7E-07 | Hair, eye color | ||
| 16q24.3 | CDK10 | rs258322 | 1.37 (1.22, 1.55) | 2.1E-07 | Hair color, melanoma | ||
| 20q11.21 | CDK5RAP1 | rs291671 | 1.39 (1.24, 1.57) | 7.0E-08 | Hair color | ||
| Nonmelanoma skin cancer | 1,931 | 6p25.3 | IRF4 | rs12203592a | 1.50 (1.36, 1.64) | 3.8E-17 | Hair, eye color, freckling, PSP |
| 11q14.3 | TYR | rs1847134a | 1.28 (1.18, 1.38) | 2.6E-10 | Eye color | ||
| Seborrheic keratosis | 2,570 | 5p15.33 | TERT | rs2853676 | 0.80 (0.74, 0.87) | 1.6E-07 | Glioma |
| Lipoma | 214 | 3p21.1 | ITIH1 | rs1042779 | 0.70 (0.61, 0.81) | 9.9E-07 | Bipolar disorder |
| Hypercoagulable state | 91 | 1q24 | NME7 | rs16861990b | 3.71 (2.57, 5.34) | 2.0E-12 | D-dimer levels |
| Bronchiectasis | 144 | 1q32.1 | KIF21B | rs2297909 | 1.81 (1.43, 2.29) | 8.7E-07 | Ankylosing spondylitis |
Novel associations with P < 4.6 × 10−6 are reported. For highly related sub-phenotypes (e.g., skin cancer and nonmelanoma skin cancer), only the strongest association is reported. Associations potentially in linkage disequilibrium with known associations are excluded here. All novel associations with P < 4.6 × 10−6 can be found in Supplementary Table 8. PSP, progressive supranuclear palsy.
a
Other studies have demonstrated associations with squamous cell carcinoma and potentially basal cell carcinoma (P > 1 × 10−4)23,24.
b
This SNP is in weak LD with the Factor V Leiden mutation (rs6025, r2 = 0.05 per 1,000 genomes).