Table 1. Haplotype frequencies in cases and controls of AS-associated SNPs at IL23R–IL12RB2 intergenic region.
| Haplotypes | Immunochip controls (n=19 400), n (%)a | Immunochip AS cases (n=8460), n (%)a | rs11209026 (risk=G) | rs11209032 (risk=A) | rs6677188 (risk=A) | rs924080 (risk=T) | rs11578380 (risk=G) | OR | P-valueb |
|---|---|---|---|---|---|---|---|---|---|
| 1 | 10 (0.05) | 6 (0.07) | G | G | A | T | C | 1.4 | 0.5 |
| 2 | 6204 (31.98) | 3056 (36.12) | G | A | T | T | C | 1.5 | <2 × 10−21 |
| 3 | 27 (0.14) | 6 (0.07) | A | G | T | T | C | 0.5 | 0.1 |
| 4 | 2272 (11.71) | 929 (10.98) | G | G | T | T | C | 0.9 | 0.06 |
| 5 | 34 (0.18) | 11 (0.13) | A | G | A | C | G | 0.7 | 0.4 |
| 6 | 4887 (25.19) | 2047 (24.20) | G | G | A | C | G | 0.9 | 0.3 |
| 7 | 1224 (6.31) | 320 (3.78) | A | G | T | C | G | 0.6 | <3 × 10−18 |
| 8 | 2718 (14.01) | 1202 (14.21) | G | G | T | C | G | 1.0 | 0.6 |
| 9 | 204 (1.05) | 98 (1.16) | G | A | T | T | G | 1.1 | 0.4 |
| 10 | 1774 (9.14) | 764 (9.03) | G | G | T | T | G | 1.0 | 0.7 |
Abbreviations: AS, ankylosing spondylitis; OR, odds ratio; SNP, single-nucleotide polymorphism.
a
PLINK analysis for haplotype estimation excludes very rare haplotypes that exist in <0.05% of the population.
b
χ2-test performed on Immunochip cases versus controls.