Table 1.
Genes with significant association to AA
| Region | Gene | Function | Strongest association (P value) | Maximum odds ratio | Involved in other autoimmune disease |
|---|---|---|---|---|---|
| 2q33.2 | CTLA4 | Co-stimulatory family | 3.55 × 10−13 | 1.44 | T1D, RA, CeD, MS, SLE, GD |
| ICOS | Co-stimulatory family | 4.33 × 10−8 | 1.32 | ||
| 4q27 | IL-21/IL-2 | T-, B- and NK-cell proliferation | 4.27 × 10−8 | 1.34 | T1D, RA, CeD, PS |
| 6q25.1 | ULBP6 | NKG2D activating ligand | 4.49 × 10−19 | 1.65 | None |
| ULBP3 | NKG2D activating ligand | 4.43 × 10−17 | 1.52 | None | |
| 9q31.1 | STX17 | Premature hair greying | 3.60 × 10−7 | 1.33 | None |
| 10p15.1 | IL-2RA | T-cell proliferation | 1.74 × 10−12 | 1.41 | T1D, MS, GD, GV |
| 11q13 | PRDX5 | Antioxidant enzyme | 4.14 × 10−7 | 1.33 | MS |
| 12q13 | Eos (IKZF4) | Treg transcription factor | 3.21 × 10−8 | 1.34 | T1D, SLE |
| ERBB3 | Epidermal growth factor receptor | 1.27 × 10−7 | 1.34 | T1D, SLE | |
| 6p21.32 | MICA | NKG2D activating ligand | 1.19 × 10−7 | 1.44 | T1D, RA, CeD, UC, PS, SLE |
| (HLA) | NOTCH4 | Haematopoietic differentiation | 1.03 × 10−8 | 1.61 | T1D, RA, MS |
| C6orf10 | Unknown | 1.45 × 10−16 | 2.36 | T1D, RA, PS, GV | |
| BTNL2 | Co-stimulatory family | 2.11 × 10−26 | 2.70 | T1D, RA, UC, CD, SLE, MS, GV | |
| HLA-DRA | Antigen presentation | 2.93 × 10−31 | 2.62 | T1D, RA, CeD, MS, GV | |
| HLA-DQA1 | Antigen presentation | 3.60 × 10−17 | 2.15 | T1D, RA, CeD, MS, SLE, PS, CD, UC, GD | |
| HLA-DQA2 | Antigen presentation | 1.38 × 10−35 | 5.43 | T1D, RA | |
| HLA-DQB2 | Antigen presentation | 1.73 × 10−13 | 1.60 | RA |
Each of the eight regions implicated in our study contains multiple significant SNPs, which are detailed in Supplementary Tables 1 and 2. Here we display candidate genes within the implicated regions, and include the P value of the most significant SNP, and the odds ratio for the SNP with the largest effect estimate. Diseases are listed for which a GWAS or previous candidate gene study identified the same region (http://www.genome.gov/gwastudies, http://www.cdc.gov/genomics/hugenet): Crohn’s disease (CD), celiac disease (CeD), Graves disease (GD), generalized vitiligo (GV), multiple sclerosis (MS), psoriasis (PS), rheumatoid arthritis (RA), system lupus erythematosus (SLE), type I diabetes (T1D), and ulcerative colitis (UC).