Table 1.
Chromo-some locus | SNP | Position (bp)* | A1 | A2 | Nearest gene | Ensembl annotation | MAF | P-value | OR (95% CI) | r2** |
---|---|---|---|---|---|---|---|---|---|---|
6p21.3 | rs9270911†‡ | 32,572,202 | T | C | HLA-DRB1 | Regulatory region variant | 0.4413 | 5.512E−10 | 1.53 (1.34 –1.74) | 1 |
6p21.3 | rs6906021† | 32,626,311 | C | T | HLA-DQB1 | Downstream gene variant | 0.4406 | 3.478E−09 | 1.50 (1.31 –1.72) | 0.49 |
6p21.3 | rs1129740 | 32,609,105 | G | A | HLA-DQA1 | Missense variant | 0.4889 | 3.657E−09 | 0.67 (0.59–0.77) | 0.76 |
6p21.3 | rs482205†‡ | 32,576,009 | G | T | HLA-DRB1 | Intergenic variant | 0.3621 | 3.754E−09 | 1.51 (1.32–1.73) | 0.54 |
6p21.3 | rs1063355¥ | 32,627,714 | T | G | HLA-DQB1 | 3′UTR variant | 0.4894 | 3.831E−09 | 0.67 (0.59–0.77) | 0.76 |
6p21.3 | rs9273349¥ | 32,625,869 | T | C | HLA-DQB1 | Downstream gene variant | 0.4894 | 3.831E−09 | 0.67 (0.59–0.77) | 0.76 |
6p21.3 | rs643889 | 32,575,918 | T | A | HLA-DRB1 | Intergenic variant | 0.3614 | 3.996E−09 | 1.51 (1.32–1.74) | 0.53 |
6p21.3 | rs477515 | 32,569,691 | A | G | HLA-DRB1 | Intergenic variant | 0.3338 | 5.033E−09 | 1.51 (1.32–1.74) | 0.64 |
6p21.3 | rs2516049 | 32,570,400 | C | T | HLA-DRB1 | Intergenic variant | 0.3343 | 5.847E−09 | 1.51 (1.32–1.74) | 0.64 |
6p21.3 | rs17205647 | 32,637,418 | A | G | HLA-DQB1 | Upstream gene variant | 0.3721 | 1.177E−08 | 1.48 (1.30–1.69) | 0.35 |
6p21.3 | rs1071630 | 32,609,126 | T | C | HLA-DQA1 | Missense variant | 0.4862 | 1.207E−08 | 0.68 (0.60–0.78) | 0.75 |
6p21.3 | rs6928482† | 32,626,249 | C | T | HLA-DQB1 | Downstream gene variant | 0.4447 | 1.482E−08 | 1.48 (1.29–1.69) | 0.48 |
6p21.3 | rs17843604¥ | 32,620,283 | T | C | HLADQA1 | Intergenic variant | 0.4888 | 1.497E−08 | 1.47 (1.29–1.68) | 0.8 |
6p21.3 | rs4538748 | 32,657,505 | C | T | HLADQA1 | Intergenic variant | 0.3743 | 2.377E−08 | 1.46 (1.28 –1.67) | 0.34 |
SNP, single nucleotide polymorphism; A1, minor allele; A2, major allele; MAF, minor allele frequency; HWE, Hardy–Weinberg equilibrium.
*The position is based on the University of California Santa Cruz (UCSC) human genome build 19 (hg19/GRCCh37).
**r2:linkage disequilibrium (LD) with the lead SNP rs9270911.
†Independent SNPs (podoconiosis-associated SNPs that were independent of each other (r2 < 0.6) within 500 kb sliding windows, identified during annotation (see methods).
‡Lead SNPs: independent SNPs that are independent from each other (r2 < 0.1).
¥SNPs that showed suggestive genome-wide linkage with podoconiosis in the first GWAS16.