Table 1. Independent classical HLA alleles and SNPs in Hispanics.
| Allele/SNP | Model | Freq (Allele) | OR (L95-U95)‡ | P | Amino Acid in LD (R2>0.8) | Best SNP Tag | SNP R2 | Gene | Function |
|---|---|---|---|---|---|---|---|---|---|
| DQB1*06:02 | Dom | 0.08 | 2.70 (2.23–3.27) | 2.66E-24 | None | rs9273342 | 0.99 | ||
| A*02:01 | Add | 0.19 | 0.69 (0.59–0.80) | 2.72E-06 | A_95_29911057_exon3_V | rs2844821 | 0.89 | ||
| DPB1*03:01 | Add | 0.07 | 1.53 (1.24–1.87) | 5.36E-05 | None | DPB1-2939-33046757-intron1 | 0.85 | ||
| DRB1*13:03 | Add | 0.02 | 2.25 (1.52–3.34) | 5.05E-05 | None | rs75589097 | 0.94 | ||
| DQB1*02:01 | Add | 0.21 | 1.36 (1.18–1.57) | 2.80E-05 | (DQB1)* _-10_32634317_exon1_S; _74_32632630_exon2_A; _71_32632639_exon2_K; _55_32632687_exon2_L; _37_32632741_exon2_I; _30_32632762_exon2_S; _-10_32634317_exon1_A; _37_32632741_exon2_Y |
DQB1-6203-32628182-intron5 | 1 | ||
| DRB1*15:01 | Add | 0.07 | 1.83 (1.28–2.62) | 9.63E-04 | None | rs9269243 | 0.99 | ||
| rs371143509 | Dom | 0.09 (T) | 0.55 (0.43–0.71) | 2.44E-06 | None | MICB | intron | ||
| rs6929950† | Add | 0.04 (C) | 0.42 (0.29–0.61) | 6.06E-06 | None | OR5V1 | intron | ||
| rs112394499 | Dom | 0.10 (T) | 1.62 (1.32–2.01) | 6.82E-06 | None | HCG24 | nc-transcript | ||
| rs2844503 | Add | 0.48 (A) | 1.34 (1.17–1.52) | 1.72E-05 | None | HCG26 / MICB-DT | intergenic | ||
| rs6902067 | Rec | 0.34 (A) | 0.52 (0.39–0.71) | 3.46E-05 | None | MICA / MICB | intergenic | ||
| rs3021302 | Rec | 0.14 (C) | 3.18 (1.83–5.52) | 4.16E-05 | None | HLA-DQA1 / DQB1 | intergenic |
† indicates a novel variant in Hispanics
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)