Table 1. PheWAS phenotypes associated with SNP variation in the HLA region*.
| PheWAS disease | Genetic liability (s.e.)† | P-value† | Class I‡ | Class II‡ | Other HLA‡ |
|---|---|---|---|---|---|
| Known associations | |||||
| Ankylosing spondylitis | 0.074 (0.013) | <1.0 × 10−20 | 0.0006§ | 1 | 0.012 |
| Type I diabetes | 0.099 (0.014) | <1.0 × 10−20 | 1 | 0.00002§ | 0.0033§ |
| Rheumatoid arthritis | 0.035 (0.008) | <1.0 × 10−20 | 1§ | 0.005§ | 0.041§ |
| Multiple sclerosis | 0.023 (0.006) | <1.0 × 10−20 | 0.68§ | 0.01§ | 0.23§ |
| Hypothyroidism | 0.009 (0.003) | 5.6 × 10−9 | 0.7§ | 0.067 | 0.13§ |
| Psoriasis | 0.017 (0.005) | 6.5 × 10−9 | 0.044§ | 0.97 | 0.17 |
| Juvenile rheumatoid arthritis | 0.025 (0.008) | 1.1 × 10−8 | 0.21 | 0.026§ | 0.42 |
| Primary biliary cirrhosis | 0.017 (0.006) | 6.7 × 10−8 | 0.41 | 0.057§ | 0.19 |
| Coeliac disease | 0.008 (0.004) | 3.8 × 10−7 | 1 | 0.062§ | 0.31 |
| Macular degeneration | 0.013 (0.005) | 3.2 × 10−5 | 1 | 1 | 0.014§ |
| Ulcerative colitis|| | 0.007 (0.003) | 3.9 × 10−5 | n/a | n/a§ | n/a§ |
| Systemic lupus erythematosus | 0.005 (0.003) | 2.7 × 10−4 | 0.89 | 0.59§ | 0.22§ |
| Premature menopause | 0.006 (0.003) | 1.0 × 10−3 | 0.72 | 0.72 | 0.25§ |
| Novel associations | |||||
| Sicca syndrome | 0.009 (0.004) | 1.8 × 10−6 | 1 | 0.14 | 0.28 |
| Dermatomyositis and polymyositis | 0.008 (0.004) | 1.1 × 10−5 | 0.11 | 0.88 | 0.61 |
| Polymyalgia rheumatica | 0.010 (0.005) | 3.5 × 10−4 | 1 | 0.8 | 0.042 |
| Cholangitis | 0.006 (0.004) | 5.8 × 10−4 | 0.38 | 1 | 0.17 |
| Dermatophytosis of the body | 0.004 (0.003) | 6.8 × 10−4 | 1 | 1 | 0.16 |
*Only phenotypes with an FDR q<0.05 and that mapped to the GWAS Catalog or have unreported associations are shown.
†From a multivariable GLMM analysis that incorporated a HLA and non-HLA GRM and adjusted for age and sex each of the PheWAS phenotypes. P-values correspond to the HLA variance component.
‡Shown are P-values from a multivariable GLMM analysis incorporating GRMs comprising SNPs within the specificied HLA region (see Methods).
||An estimate could not be obtained because the statistical model did not converge.
§A SNP association with a P-value<5 × 10−8 in the GWAS Catalog reported in the specified region.