Table 2. Independent classical HLA alleles and SNPs in African Americans.
| Allele/SNP | Model | Freq (Allele) | OR (L95-U95)‡ | P | Amino Acid in LD (R2>0.8) | Best SNP Tag | SNP R2 | Gene | Function |
|---|---|---|---|---|---|---|---|---|---|
| DRB1*15:01 | Dom | 0.03 | 1.91 (1.41–2.59) | 3.48E-05 | none | rs9269243 | 0.99 | ||
| A*02:01 | Add | 0.13 | 0.68 (0.57–0.82) | 5.07E-05 | AA_95_29911057_exon3_V | rs12153924 | 0.98 | ||
| B*53:01 | Dom | 0.12 | 0.68 (0.55–0.84) | 3.22E-04 | none | rs115219755 | 0.92 | ||
| rs760145 | Add | 0.45 (T) | 0.75 (0.66–0.85) | 7.75E-06 | none | HLA-F-AS1 | Intron | ||
| rs28371315 | Rec | 0.34 (C) | 0.52 (0.39–0.70) | 8.85E-06 | none | HLA-DQB1 / DQA2 | Intergenic | ||
| rs2516423 | Dom | 0.50 (A) | 0.64 (0.53–0.79) | 1.59E-05 | none | MICB-DT | intron |
‡ indicates a novel variant in African Americans
Model: Add = Additive, Dom = Dominant, Rec = Recessive
‡ Reported odds ratios and 95% confidence intervals are sequential as identified in the stepwise regression model such that the effect size for each allele/SNP is reported after conditioning on the alleles/SNPs in the preceding rows
Gene has been annotated with ANNOVAR version date June 2020 (Wang et al., Nucleic Acids Research, 2010)