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. Author manuscript; available in PMC: 2014 Mar 28.
Published in final edited form as: Nat Biotechnol. 2013 Dec;31(12):1102–1110. doi: 10.1038/nbt.2749

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).