Table 2.
Independent giant cell arteritis-associated HLA variants after conditional analysis
| Base pair (hg38) | Nearest gene | Amino acid variant in highest LD (r2) | Classical HLA allele in highest LD (r2) | Effect allele | Patient minor allele frequency | Control minor allele frequency | p value* | Conditional p value† | OR (95% CI) | |
|---|---|---|---|---|---|---|---|---|---|---|
| rs17882084 | 32581836 | HLA-DRB1 | DRB1-180-Leu (0·999); DRB1-96-Tyr (0·999) | HLA-DRB1*04 (0·984) | A | 0·26 | 0·16 | 4·34 × 10−87 | .. | 2·02 (1·89–2·15) |
| rs1049087 | 32662112 | HLA-DQB1 | DQB1-57-Ala (0·726) | HLA-DQA1*01 (0·424); HLA-DQB1*02 (0·422) | A | 0·51 | 0·41 | 7·70 × 10−44 | 1·07 × 10−21 | 1·49 (1·42–1·58) |
| rs2856726 | 32698944 | Intergenic | DQB1-167-His (0·443); DQB1-13-Gly (0·443) | HLA-DQB1*0301 (0·419) | A | 0·41 | 0·36 | 1·35 × 10−7 | 3·75 × 10−8 | 1·17 (1·10–1·24) |
| rs2596501 | 31353434 | HLA-B | B-97-Ser/Asn/Val (0·499); B-45-Thr/Lys (0·384) | HLA-C*07 (0·171) | G | 0·50 | 0·48 | 2·79 × 10−10 | 1·16 × 10−7 | 1·20 (1·14–1·27) |
| HLA-DPB1*03 | 33081591 | HLA-DPB1 | DPB1-57-Asp (0·593); DPB1-65-Leu (0·570) | .. | .. | 0·08 | 0·11 | 3·60 × 10−7 | 4·37 × 10−7 | 0·77 (0·70–0·85) |
LD=linkage disequilibrium. OR=odds ratio.
*
p values of the meta-analysis.
†
p values of the meta-analysis after stepwise conditional analysis, including previous associated signals.