Table 1. Genomic regions with the strongest association signals for celiac disease.
| Cytogenetic location | Position (bp) | SNP | Rank UKGWAS | P UKGWAS | P follow-up | Odds ratioa follow-up [95% CI] | P overall | Putative candidate genesb |
|---|---|---|---|---|---|---|---|---|
| Sample size | n=2189 | n=5049 | n=7238 | |||||
| Assay chemistry | Infinium | GoldenGate | ||||||
| 1q31 | 190803436 | rs2816316 | 382 | 0.0012 | 5.11 × 10-9 | 0.71 [0.63 - 0.80] | 2.58 × 10-11 | RGS1 |
| 2q11-2q12 | 102338297 | rs13015714 | 149 | 0.00041 | 2.66 × 10-6 | 1.27 [1.15 - 1.40] | 4.37 × 10-9 | IL1RL1, IL18R1, IL18RAP, SLC9A4 |
| 102437000 | rs917997 | 41 | 9.06 × 10-5 | 1.97 × 10-6 | 1.27 [1.15 - 1.40] | 8.49 × 10-10 | ||
| 3p21 | 46327388 | rs6441961 | 1004 | 0.0028 | 3.21 × 10-5 | 1.21 [1.10 - 1.32] | 3.14 × 10-7 | CCR1, CCR3 |
| 3q25 - 3q26 | 161147744 | rs17810546 | 111 | 0.00034 | 7.77 × 10-7 | 1.34 [1.19 - 1.51] | 1.07 × 10-9 | IL12A, SCHIP1 |
| 161179692 | rs9811792 | 898 | 0.0028 | 5.42 × 10-6 | 1.21 [1.12 - 1.32] | 5.24 × 10-8 | ||
| 3q28 | 189570322 | rs9851967 | 453 | 0.00091 | 7.13 × 10-6 | 0.82 [0.76 - 0.90] | 2.45 × 10-8 | LPP |
| 189571948 | rs13076312 | 186 | 0.00034 | 1.21 × 10-5 | 1.21 [1.11 - 1.31] | 1.78 × 10-8 | ||
| 189595248 | rs1464510 | 52 | 7.65 × 10-5 | 1.21 × 10-5 | 1.21 [1.11 -1.31] | 5.33 × 10-9 | ||
| 189607048 | rs1559810 | 59 | 0.00010 | 3.28 × 10-5 | 1.19 [1.10 - 1.30] | 1.99 × 10-8 | ||
| 4q27 | 123292459 | rs11938795 | 88 | 0.00026 | 1.07 × 10-5 | 0.80 [0.73 - 0.89] | 1.30 × 10-8 | IL2, IL21 |
| 123334952 | rs13151961 | 10 | 5.48 × 10-6 | 4.32 × 10-8 | 0.72 [0.65 - 0.81] | 1.53 × 10-12 | ||
| 123437763 | rs13119723 | 1 | 2.51 × 10-7 | 1.23 × 10-7 | 0.73 [0.65 - 0.82] | 5.94 × 10-13 | ||
| 123447563 | rs11734090 | 106 | 0.00034 | 2.95 × 10-5 | 0.81 [0.74 - 0.90] | 4.76 × 10-8 | ||
| 123560609 | rs7684187 | 245 | 0.00091 | 3.11 × 10-5 | 0.82 [0.75 - 0.90] | 1.13 × 10-7 | ||
| 123727951 | rs12642902 | 25 | 4.59 × 10-5 | 7.35 × 10-6 | 0.82 [0.75 - 0.89] | 2.12 × 10-9 | ||
| 123728871 | rs6822844 | 7 | 4.80 × 10-6 | 9.84 × 10-9 | 0.71 [0.63 - 0.80] | 2.82 × 10-13 | ||
| 123774157 | rs6840978 | 31 | 4.79 × 10-5 | 2.32 × 10-7 | 0.75 [0.68 - 0.84] | 5.53 × 10-11 | ||
| 6q25 | 159385965 | rs1738074 | 503 | 0.0016 | 1.19 × 10-5 | 1.21 [1.11 - 1.31] | 6.71 × 10-8 | TAGAP |
| 12q24 | 110368991 | rs3184504c | 318 | 0.0011 | 3.22 × 10-5 | 1.19 [1.10 - 1.30] | 1.33 × 10-7 | SH2B3(LNK), ATXN2 |
| 110492139 | rs653178 | 207 | 0.00065 | 2.98 × 10-5 | 1.19 [1.10 - 1.30] | 8.00 × 10-8 | ||
Cochran-Mantel-Haenszel association analysis of 1020 SNPs (excluding HLA region). SNPs with P overall < 5 × 10-7 (the WTCCC threshold for reporting possible associations7) are shown. Association statistics are reported for twenty one SNPs from eight regions, including the previously reported IL2/IL21 region. Chromosomal positions based on NCBI build-36 coordinates. Data from the UKGWAS was re-analysed with removal of a small number of first degree relatives compared to previous publication2.
Odds ratios for the UKGWAS ,and overall study are reported in Supplementary Data 1.
Named genes either map to the same strong LD block as associated SNPs, or the SNPs physically map within the gene - causality is not proven.
rs3184504 is a non-synonymous SNP in SH2B3 (R262W).