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. 2021 Feb 8;11:3285. doi: 10.1038/s41598-021-81836-x

Table 1.

Genome-wide significant results from a genome-wide association study (GWAS) on podoconiosis undertaken in three ethnic groups (Amhara, Oromo and Wolaita, dataset 1) from Ethiopia.

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.