Table 2. Sequence variants showing genome-wide significant association with Tuberculosis in Iceland.
For each sequence variant the reference SNP ID number (rs#), chromosome (Chr), hg18 position, its effect on a gene (Coding effect), minor allele frequency (MAF), gene name and modeled allele are provided in addition to the odds ratio (OR) for tuberculosis and the corresponding P values.
| Pulmonary TB | Tuberculosis | M. tuberculosis infection (including TB) | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| N=3,686 | N=8,162 | N=14,724 | ||||||||||||||
| rs# | chr | pos | MAF (%) | Info | coding | gene | Effect allele | P | OR | 95% CI | P | OR | 95% CI | P | OR | 95% CI |
| rs557011 | chr6 | 32694991 | 40.2 | 0.997 | - | - | T | 5.8×10-12 | 1.25 | [1.17-1.33] | 3.7×10-9 | 1.15 | [1.10-1.20] | 3.1×10-13 | 1.14 | [1.10-1.18] |
| rs9271378 | chr6 | 32695278 | 32.5 | 0.998 | - | - | G | 2.5×10-12 | 0.78 | [0.73-0.84] | 1.2×10-9 | 0.86 | [0.82-0.90] | 1.3×10-7 | 0.90 | [0.87-0.94] |
| rs9272785 | chr6 | 32718379 | 19.1 | 0.996 | p.Ala210Thr* | HLA-DQA1 | A | 3.5×10-7 | 1.22 | [1.13-1.32] | 7.3×10-4 | 1.10 | [1.04-1.16] | 9.3×10-9 | 1.14 | [1.09-1.19] |
*
p.Thr49Ser (rs1048023) , p.Gly79Ser (rs12722072) and p.Met99Val (rs1064944) correlate (r2=0.99) with rs9272785/p.Ala210Thr and show identical association.