Loci associated with inflammatory bowel disease that were significantly different between First Nations and white participants
| Function; SNP | Locus | Risk allele | Risk allele frequency | Odds ratio | p value (corrected*) | |
|---|---|---|---|---|---|---|
| First Nations participants | White participants | |||||
| Bacterial sensing and autophagy | ||||||
| rs3828309 | ATG16L1 | G | 0.116 | 0.516 | 0.13 | 3.5 × 10−30 |
| rs2241880 | ATG16L1 | C | 0.115 | 0.518 | 0.13 | 4.1 × 10−30 |
| rs3792106 | ATG16L1 | C | 0.178 | 0.566 | 0.16 | 5.1 × 10−28 |
| rs11747270 | IRGM | C | 0.165 | 0.084 | 2.01 | 1.1 × 10−2 |
| rs2066844 | NOD2 (R702W) | T | 0.009 | 0.035 | 0.25 | 0.2† |
| rs2066845 | NOD2 (G908R) | G | 0 | 0.016 | NA | > 0.9† |
| rs2066847 | NOD2 (3020insC) | C (ins) | 0.010 | 0.032 | 0.34 | > 0.9† |
| rs5743289 | NOD2 | T | 0.040 | 0.158 | 0.22 | 1.4 × 10−8 |
| rs2076756 | NOD2 | G | 0.046 | 0.251 | 0.13 | 1.1 × 10−17 |
| rs10521209 | NOD2 | A | 0.875 | 0.627 | 4.16 | 4.0 × 10−17 |
| Interleukin-23 pathway | ||||||
| rs11465804 | IL23R | T | 0.987 | 0.945 | 4.57 | 1.4 × 10−2 |
| rs10045431 | IL12B | G | 0.919 | 0.695 | 4.98 | 1.2 × 10−16 |
| Immunological synapse/co-stimulatory pathways | ||||||
| rs762421 | ICOSLG | G | 0.815 | 0.379 | 7.26 | 7.9 × 10−31 |
| rs3763313 | BTNL2, SLC26A3, HLA- DRB1, HLA-DQA1 | C | 0.281 | 0.169 | 2.00 | 4.1 × 10−4 |
| rs9268480 | BTNL2 | G | 0.634 | 0.749 | 0.59 | 4.0 × 10−3 |
| rs2395185 | BTNL2 to HLA-DQB1 | G | 0.528 | 0.726 | 0.42 | 4.1 × 10−9 |
| rs9263739 | HLA | A | 0.043 | 0.191 | 0.19 | 2.7 × 10−11 |
| rs6478108 | TNFSF15 | A | 0.826 | 0.683 | 2.27 | 1.6 × 10−6 |
| rs4263839 | TNFSF15 | G | 0.822 | 0.706 | 1.97 | 2.3 × 10−4 |
| Other | ||||||
| rs4613763 | PTGER4 | C | 0.024 | 0.105 | 0.25 | 9.2 × 10−5 |
| rs3197999 | MST1 | T | 0.096 | 0.298 | 0.25 | 8.5 × 10−14 |
| rs10995271 | ZNF365 | C | 0.146 | 0.424 | 0.24 | 4.5 × 10−19 |
| rs7927894 | C11orf30 | A | 0.111 | 0.387 | 0.20 | 3.7 × 10−20 |
| rs11175593 | LRRK2, MUC19 | T | 0.303 | 0.035 | 11.67 | 8.7 × 10−19 |
| rs2542151 | PTPN2 | G | 0.069 | 0.165 | 0.38 | 5.2 × 10−5 |
| Unknown‡ | ||||||
| rs9286879 | 1q24 | G | 0.806 | 0.247 | 11.21 | 3.4 × 10−37 |
| rs3806308 | 1p36 | G | 0.448 | 0.621 | 0.48 | 4.6 × 10−7 |
| rs6426833 | 1p36 | T | 0.407 | 0.531 | 0.63 | 4.0 × 10−3 |
| rs2188962 | 5q31 | T | 0.095 | 0.424 | 0.14 | 3.2 × 10−26 |
| rs17582416 | 10p11 | G | 0.105 | 0.305 | 0.29 | 1.3 × 10−12 |
| rs17085007 | 13q12 | G | 0.055 | 0.176 | 0.28 | 8.9 × 10−8 |
Note: NA = not applicable, SNP = single nucleotide polymorphism.
↵* Bonferroni correction for multiple testing.
↵† NOD2 risk score combining important variants (R702W, G908R, 3020insC) was significantly lower among First Nations participants (p < 0.0001). The p values for the individual variants before Bonferroni correction were p = 0.0034 for R702W, p > 0.9 for G908R and p = 0.016 for 3020insC.
↵‡ SNPs associated with inflammatory bowel disease for which no candidate gene has been described, in regions of the genome that lack identifiable genes (gene deserts).