Significant PheWAS associations (p≤5.7E-08) with ‘GWAS significant’ SNPs
| SNP | Position (bp,hg19) | Gene | Cases (MAF) | Controls (MAF) | OR (95% CI) | Fisher's p value | FDR | ICD9 Code | PheWAS Phenotype | GWAS Phenotype1 | Reported OR ranges1 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| rs9264942 | 31 274 380 | HLA-C, HLA-B | 327 (0.46) | 6744 (0.35) | 1.6 (1.4 to 1.9) | 5.8E-09 | 0.0026 | 696 | Psoriasis and similar disorders | Crohn's disease, HIV-1 control | 1.2–2.9, 5.3 |
| 253 (0.48) | 7034 (0.35) | 1.7 (1.4 to 2.0) | 5.5E-09 | 0.0026 | 696.1 | Other psoriasis | |||||
| rs10484554 | 31 274 555 | HLA-C, HLA-B | 327 (0.25) | 6744 (0.14) | 2.0 (1.7 to 2.4) | 9.2E-13 | 1.5E-6 | 696 | Psoriasis and similar disorders | Psoriasis, AIDS progression | 2.8–4.7, NR |
| 42 (0.40) | 7376 (0.14) | 4.2 (2.7 to 6.4) | 1.9E-09 | 0.001 | 696.0 | Psoriatic arthropathy | |||||
| 253 (0.28) | 7034 (0.14) | 2.4 (1.9 to 2.9) | 2.1E-15 | 5.7E-9 | 696.1 | Other psoriasis | |||||
| rs4349859 | 31 365 787 | HLA-B, MICA | 35 (0.39) | 7383 (0.04) | 14.5 (8.9 to 23.6) | 1.5E-19 | 2.5E-12 | 720.0 | Ankylosing spondylitis | Ankylosing spondylitis | 40.831 |
| 180 (0.16) | 7238 (0.04) | 4.2 (3.2 to 5.7) | 8.7E-17 | 7.3E-10 | 720 | Ankylosing spondylitis and other inflammatory spondylopathies | |||||
| 26 (0.40) | 7392 (0.04) | 15.6 (8.9 to 27.3) | 4.1E-16 | 1.7E-09 | 720.8 | Other inflammatory spondylopathies | |||||
| 26 (0.40) | 7392 (0.04) | 15.6 (8.9 to 27.3) | 4.1E-16 | 1.7E-09 | 720.89 | Other inflammatory spondylopathies | |||||
| 30 (0.37) | 7388 (0.04) | 13.3 (7.8 to 22.7) | 9.7E-16 | 3.2E-09 | 720.9 | Unspecified inflammatory spondylopathy | |||||
| rs4418214 | 31 391 401 | MICA, HCP5 | 253 (0.16) | 7034 (0.08) | 2.3 (1.8 to 2.9) | 8.0E-10 | 5.6E-04 | 696.1 | Other psoriasis | HIV-1 susceptibility, HIV-1 control | 1.5, 4.4 |
| 35 (0.41) | 7383 (0.08) | 8.2 (5.1 to 13.2) | 1.5E-14 | 3.6E-08 | 720.0 | Ankylosing spondylitis | |||||
| 180 (0.19) | 7238 (0.08) | 2.6 (2.0 to 3.5) | 1.8E-10 | 1.5E-04 | 720 | Ankylosing spondylitis and other inflammatory spondylopathies | |||||
| 26 (0.42) | 7392 (0.08) | 8.3 (4.6 to 14.7) | 1.2E-10 | 1.1E-04 | 720.8 | Other inflammatory spondylopathies | |||||
| 26 (0.42) | 7392 (0.08) | 8.3 (4.6 to 14.7) | 1.2E-10 | 1.1E-04 | 720.89 | Other inflammatory spondylopathies | |||||
| 30 (0.40) | 7388 (0.08) | 7.7 (4.6 to 13.0) | 5.8E-12 | 8.1E-06 | 720.9 | Unspecified inflammatory spondylopathy | |||||
| rs9368699 | 31 802 541 | C6orf48, SNORD48 | 253 (0.09) | 7034 (0.04) | 2.7 (1.9 to 3.6) | 3.3E-08 | 0.011 | 696.1 | Other psoriasis | HIV-1 control | NR |
| rs2071278 | 32 165 444 | NOTCH4 | 47 (0.40) | 7371 (0.16) | 3.5 (2.3 to 5.2) | 1.8E-08 | 0.0071 | 579.0 | Coeliac disease | Complement factor C3 and C4 levels | 0.1 |
| rs3131296 | 32 172 993 | NOTCH4 | 47 (0.38) | 7371 (0.14) | 3.8(2.5 to 5.8) | 3.3E-09 | 0.0016 | 579.0 | Coeliac disease | Schizophrenia | 1.2 |
| rs2187668 | 32 605 884 | HLA-DQA1 | 47 (0.34) | 7371 (0.12) | 3.8 (2.4 to 5.8) | 1.9E-08 | 0.0072 | 579.0 | Coeliac disease | Coeliac disease, systemic lupus erythematosus, nephropathy (idiopathic membranous), IgA | 6.2–7.0, 2.2, 4.3, 2.5 |
| rs1794275 | 32 671 248 | HLA-DQB1, HLA-DQA2 | 97 (0.34) | 7321 (0.17) | 2.5 (1.8 to 3.4) | 1.8E-08 | 0.0071 | 697.0 | Lichen planus | IgA nephropathy | 1.3 |
Reported OR ranges are from the GWAS Catalog1 unless otherwise specified.
FDR, false discovery rate; GWAS, genome-wide association study; ICD9, International Classification of Disease V.9; MAF, minor allele frequency; NR, not reported; PheWAS, phenome-wide association study.