Table 3. Association Results of Type 1 Diabetes Loci Tested in Celiac Disease.
| Type 1 Diabetes Maximum 8,064 Cases and 9,339 Controls |
Celiac Disease Maximum 2,560 Cases and 9,339 Controls |
||||||||
|---|---|---|---|---|---|---|---|---|---|
| Type 1 diabetes loci/candidate gene | Minor allele |
MAF | MAF | MAF | |||||
| OR (95% CI) | P-value | UK controls |
T1D cases |
Celiac disease cases |
OR (95% CI) | P-value | |||
| 1p13/PTPN22 | rs2476601 | T | 2.05 (1.90-2.20) | 1.13 × 10−88 | 0.095 | 0.178 | 0.106 | 1.09 (0.98-1.22) | 0.130 |
| 2q24/IFIH1 | rs1990760 | G | 0.86 (0.82-0.90) | 2.13 × 10−10 | 0.389 | 0.351 | 0.397 | 1.02 (0.95-1.09) | 0.547 |
| 2q33/CTLA4 | rs3087243 | A | 0.82 (0.78-0.86) | 1.27 × 10−14 | 0.452 | 0.405 | 0.411 | 0.85 (0.80-0.90) | 1.26 × 10−6 |
| 3p21/CCR5 | rs333 | del | 0.85 (0.80-0.92) | 5.87 × 10−6 1.93 × 10−6 (2df) |
0.119 | 0.103 | 0.095 | 0.79 (0.71-0.88) | 9.18 × 10−6 |
| 4q27/IL2 | rs2069763 | T | 1.13 (1.08-1.18) | 1.28 × 10−7 | 0.329 | 0.358 | 0.346 | 1.09 (1.01-1.16) | 0.0180 |
| 5p13/IL7R | rs6897932 | A | 0.89 (0.84-0.94) | 4.13 × 10−4 | 0.274 | 0.255 | 0.254 | 0.91 (0.84-0.97) | 7.23 × 10−3 |
| 6q15/BACH2 | rs11755527 | G | 1.13 (1.09-1.18) | 8.57 × 10−9 4.37 × 10−11 (2df) |
0.465 | 0.495 | 0.491 | 1.10 (1.03-1.18) | 2.78 × 10−3 |
| 10p15/PRKCQ | rs947474 | G | 0.88 (0.83-0.93) | 1.48 × 10−5 | 0.187 | 0.171 | 0.173 | 0.90 (0.83-0.98) | 0.0178 |
| 10p15/IL2RA | rs12722495 rs11594656 |
G A |
0.62 (0.57-0.68) 0.87 (0.83-0.93) |
1.74 × 10−30 2.03 × 10−6 |
0.113 0.246 |
0.072 0.222 |
0.120 0.234 |
1.06 (0.95-1.17) 0.94 (0.87-1.01) |
0.316 0.091 |
| 11p15/INS | rs689 | A | 0.42 (0.41-0.46) | 8.93 × 10−195 1.86 × 10−202(2df) |
0.293 | 0.151 | 0.286 | 0.95 (0.89-1.03) | 0.201 |
| 12q13/ERBB3 | rs2292239 | A | 1.31 (1.22-1.34) | 5.79 × 10−22 | 0.352 | 0.407 | 0.359 | 1.02 (0.96-1.10) | 0.498 |
| 12q24/SH2B3 | rs3184504 | A | 1.28 (1.22-1.35) | 2.72 × 10−24 | 0.485 | 0.549 | 0.523 | 1.15 (1.08-1.23) | 2.85 × 10−5 |
| 15q24/CTSH | rs3825932 | C | 0.86 (0.82-0.90) | 4.62 × 10−10 | 0.318 | 0.287 | 0.334 | 1.07 (1.00-1.14) | 0.0559 |
| 16p13/CLEC16A | rs12708716 | G | 0.81 (0.77-0.86) | 3.19 × 10−13 | 0.351 | 0.306 | 0.365 | 1.06 (0.99-1.14) | 0.120 |
| 18p11/PTPN2 | rs478582 rs45450798 |
G G |
0.83 (0.79-0.88) 1.28 (1.21-1.36) |
8.83 × 10−12 1.15 × 10−16 |
0.449 0.166 |
0.408 0.202 |
0.432 0.191 |
0.93 (0.87-1.00) 1.18 (1.08-1.30) |
0.0408 2.61 × 10−4 |
| 18q22/CD226 | rs763361 | A | 1.16 (1.10-1.22) | 1.56 × 10−8 | 0.471 | 0.503 | 0.491 | 1.09 (1.02-1.16) | 0.0133 |
| 21q22/UBASH3A | rs3788013* | A | 1.13 (1.08-1.18) | 3.09 × 10−8 | 0.433 | 0.465 | 0.454 | 1.08 (1.01-1.15) | 8.88 × 10−3 |
| 22q13/C1QTNF6 | rs229541 | T | 1.12 (1.07-1.17) | 6.96 × 10−7 | 0.428 | 0.455 | 0.424 | 0.97 (0.91-1.04) | 0.423 |
The T1D results have all been published previously 1, 14, 15, except for CCR5 rs333, PTPN2 rs45450798 and IL2RA rs12722495 (Supplementary Tables 3 and 4).
*
rs3788013 is in r2 = 1 with rs876498 from Concannon et al.14 in the British case-control samples. OR = odds ratio, 95% CI = 95% confidence intervals, MAF = minor allele frequency. The MAF was estimated in a maximum of 9,339 controls, maximum of 8,064 T1D cases, and maximum of 2,560 celiac cases. The 2-df test is reported when there was a significant difference between genotypic effects model and the multiplicative allelic effects model.