Table 1.
Replication of association in multiple autoimmune diseases
| Corrected p-value | ||||||||
|---|---|---|---|---|---|---|---|---|
| Chromosome number | Cytogenetic position | Gene | SNP | Physical position | Associated diseases | Uncorrected GAW p-valuea | Adjusting with ancestry as covariate in a logistic regression model | SATb |
| 1 | 1p31 | IL23R | rs11465804 | 67414547 | CD | 1.09 × 10-3 | 1.04 × 10-3 | 2.04 × 10-3 |
| 1 | 1p13 | PTPN22 | rs2476601 | 114089610 | SLE, RA, T1D | 1.12 × 10-12 | 1.76 × 10-10 | 2.66 × 10-10 |
| 2 | 2q24 | IFIH1 | rs1990760 | 162949558 | T1D | 6.54 × 10-3 | 2.74 × 10-2 | 2.44 × 10-2 |
| 2 | 2q32.2-q32.3 | STAT4 | rs6752770 | 191681808 | RA, SLE | 7.00 × 10-3 | 1.36 × 10-2 | 3.36 × 10-2 |
| 3 | 3p21 | MST1 | rs3197999 | 49696536 | CD | 2.31 × 10-2 | 3.57 × 10-2 | 3.57 × 10-2 |
| 4 | 4q27 | KIAA1109 | rs13151961 | 123473107 | Celiac T1D, RA | 4.81 × 10-2 | 2.74 × 10-2 | 3.74 × 10-2 |
| 5 | 5p13 | PTGER4 | rs4613763 | 40428485 | CD | 1.96 × 10-3 | 7.56 × 10-3 | 5.56 × 10-3 |
| 6 | 6q23 | near TNFAIP3 | rs6933404 | 138000928 | SLE | 3.13 × 10-4 | 2.01 × 10-3 | 3.01 × 10-3 |
| 6 | 6q23 | near TNFAIP3 | rs13192841 | 138008907 | SLE | 2.93 × 10-4 | 5.71 × 10-4 | 6.47 × 10-4 |
| 6 | 6q23 | near TNFAIP3 | rs12527282 | 138008945 | SLE | 2.28 × 10-4 | 3.37 × 10-4 | 2.27 × 10-4 |
| 6 | 6q23 | near TNFAIP3 | rs2327832 | 138014761 | SLE | 1.06 × 10-4 | 7.51 × 10-4 | 6.51 × 10-4 |
| 6 | 6q23 | near TNFAIP3 | rs602414 | 138053358 | SLE | 6.03 × 10-4 | 1.29 × 10-2 | 1.29 × 10-2 |
| 6 | 6q27 | CCR6 | rs2301436 | 167408399 | CD | 1.67 × 10-2 | 1.74 × 10-2 | 4.25 × 10-2 |
| 8 | 8p23.1 | XKR6 | rs11783247 | 10826285 | SLE | 4.50 × 10-2 | 1.76 × 10-2 | 5.77 × 10-2 |
| 8 | 8p21.1 | C8orf12 | rs7836059 | 11309574 | SLE | 8.87 × 10-3 | 1.36 × 10-2 | 6.78 × 10-2 |
| 8 | 8p21.3 | C8orf13-BLK | rs2736340 | 11381382 | SLE | 1.45 × 10-5 | 2.38 × 10-5 | 0 |
| 8 | 8p21.3 | C8orf13-BLK | rs13277113 | 11386595 | SLE | 3.46 × 10-6 | 5.69 × 10-6 | 0 |
| 8 | 8p23.1 | BLK | rs2618476 | 11389950 | SLE | 3.21 × 10-6 | 4.10 × 10-6 | * c |
| 8 | 8p23.1 | BLK | rs2248932 | 11429059 | SLE | 9.79 × 10-3 | 6.49 × 10-3 | 6.69 × 10-3 |
| 9 | 9q33.2 | PHF19 | rs1953126 | 122680321 | RA | 2.76 × 10-8 | 4.97 × 10-8 | 0 |
| 9 | 9q33.2 | PHF19 | rs1609810 | 122682172 | RA | 1.79 × 10-8 | 3.38 × 10-8 | * |
| 9 | 9q33.2 | PHF19 | rs881375 | 122692719 | RA | 2.27 × 10-8 | 4.55 × 10-8 | 0 |
| 9 | 9q33.2 | PHF19 | rs6478486 | 122695150 | RA | 1.79 × 10-8 | 3.38 × 10-8 | * |
| 9 | 9q33.2 | near PHF19 | rs3761847 | 120769793 | RA | 1.24 × 10-8 | 3.88 × 10-8 | 0 |
| 9 | 9q33.2 | C5 | rs2900180 | 122776861 | RA | 6.24 × 10-9 | 1.88 × 10-8 | 0 |
| 10 | 10q24 | NKX2-3 | rs11190140 | 101281583 | CD | 4.93 × 10-2 | 8.10 × 10-2 | 8.80 × 10-2 |
| 19 | 19q13 | RSHL1 | rs8111071 | 50999246 | CD | 5.91 × 10-5 | 1.66 × 10-4 | 0 |
| 22 | 22q11.21 | UBE2L3 | rs5754217 | 20264229 | SLE | 8.94 × 10-3 | 6.34 × 10-3 | 6.57 × 10-3 |
| 22 | 22q13.2 | SCUBE1 | rs2071725 | 41934258 | SLE | 2.23 × 10-2 | 1.83 × 10-2 | 1.57 × 10-2 |
aAllelic association test
bStructured association test
c *, Imputed SNP