Table 2.
Nine genome-wide significant (p≤5×10−8) variants on chromosome 6 are associated with IBD following conditional analysis on the HLA-DRB1 SNP rs9270299 (from the UC analysis in AA). A1: tested allele; A2: Alternate allele; OR: odds ratio.
| Phenotype | Chr | Position (hg19) | Gene | SNP_Name | A1 | A2 | Combined Freq | Unconditional | Conditional | MAF (Minor Allele) | African Sub-population with highest MAF | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
| ||||||||||||||||
| OR | Pvalue | OR | P-value | YRI | EAS | EUR | SAS | |||||||||
| IBD | 6 | 32594240 | HLA-DQA1 | rs139282044 * | T | A | 0.031 | 1.93 | 9.43E-08 | 2.08 | 5.78E-09 | 0.04 (A) | 0 (A) | 0 (A) | 0 (A) | ESN - 0.08 (A) |
| 6 | 32367297 | BTNL2 | rs144540865 * | A | G | 0.032 | 1.88 | 1.41E-07 | 2.01 | 1.25E-08 | 0 (G) | 0 (G) | 0 (G) | 0 (G) | LWK - 0.03 (G) | |
| 6 | 32590316 | HLA | rs75441240 * | C | T | 0.032 | 1.84 | 2.89E-07 | 1.97 | 1.91E-08 | 0.04 (T) | 0 (T) | 0(T) | 0 (T) | ESN - 0.08 (T) | |
| 6 | 32572195 | HLA | rs140435271 * | A | G | 0.033 | 1.82 | 4.51E-07 | 1.95 | 2.97E-08 | 0.04 (G) | 0 (G) | 0 (G) | 0 (G) | ESN - 0.08 (G) | |
| 6 | 32415572 | HLA | rs114243387 * | G | C | 0.038 | 1.69 | 4.92E-07 | 1.80 | 3.25E-08 | 0.04 (C) | 0 (C) | 0 (C) | 0 (C) | ESN - 0.08 (C) | |
| 6 | 32553401 | HLA | rs144404284 | G | A | 0.048 | 1.66 | 8.14E-07 | 1.79 | 3.54E-08 | 0.05 (A) | 0.02 (A) | 0.05 (A) | 0.01 (A) | ||
| 6 | 32589502 | HLA | rs114210446 | A | G | 0.033 | 1.80 | 5.73E-07 | 1.92 | 4.11E-08 | 0.05 (G) | 0 (G) | 0.01 (G) | 0 (G) | ||
| 6 | 32425875 | HLA | rs140228374 * | C | T | 0.036 | 1.75 | 6.46E-07 | 1.87 | 4.17E-08 | 0.04 (T) | 0 (T) | 0(T) | 0 (T) | ESN - 0.08 (T) | |
| 6 | 32543575 | HLA | rs41294271 | C | T | 0.210 | 1.36 | 2.72E-06 | 1.45 | 4.27E-08 | 0.09 (T) | Observed variant without frequency or population information | ||||
Genome-wide significant (<5.0×10−8) variants associated with IBD after analysis conditioned on the HLA-DRB1 SNP rs9270299 (from the UC analysis in AA). Nine SNPs on chromosome 6 exceeded genome-wide significance for association with IBD conditioned the HLA-DRB1 SNP rs9270299 (from the UC analysis in AA). Chr: Chromosome; A1: tested allele; A2: Alternate allele; Freq: frequency; OR: odds ratio; MAF: Minor Allele Frequency.
YRI: Yoruba in Ibadan, Nigeria; EAS: East Asian; EUR: European; SAS: South Asian; LWK: Luhya in Webuye, Kenya; ESN: Esan in Nigeria; (data from 1000 genome phase 3)
African Specific SNP (monomorphic in EAS, EUR ans SAS)