Table 1.
Independent association results from the global analysis comparing scleroderma and controls after the sequential conditional analysis
| Gene | Variation | BP | N | OR (95% CI) | P value | Conditioned P value |
| HLA-DQA1 | rs1048372T* | 32 642 659 | 14 | 0.70 (0.67 to 0.73) | 1.29E-63 | – |
| HLA-DRB5/HLA-DQA1 | rs482044G | 32 608 287 | 14 | 0.73 (0.70 to 0.76) | 7.09E-50 | 1.10E-35 |
| HLA-DPB1 | rs1126511T* | 33 080 689 | 14 | 1.21 (1.16 to 1.27) | 2.01E-16 | 2.37E-25 |
| COL11A2 | rs9469378C | 33 191 887 | 14 | 1.44 (1.31 to 1.58) | 8.02E-14 | 2.16E-14 |
| HLA-DQA1 | rs1142338T* | 32 641 545 | 14 | 1.86 (1.67 to 2.07) | 3.12E-29 | 3.16E-12 |
| HLA-B/MICA | rs2844532G | 2 685 662 | 14 | 0.77 (0.73 to 0.81) | 2.11E-23 | 1.54E-11 |
| HLA-DQA2 | rs17500468G | 32 743 401 | 14 | 1.36 (1.28 to 1.43) | 1.10E-27 | 3.64E-10 |
| MICA/MICB | rs3094228G | 31 462 150 | 14 | 1.29 (1.23 to 1.36) | 1.30E-26 | 5.42E-09 |
| BTNL2/HLA-DRA | rs9268515C | 32 411 518 | 14 | 1.08 (1.03 to 1.14) | 3.01E-03 | 1.76E-09 |
| HLA-DRB1 | DRB1*11:04 | 32 584 287 | 13 | 2.11 (1.92 to 2.31) | 2.52E-56 | – |
| HLA-DQB1 | DQB1*02:02 | 32 663 284 | 14 | 0.56 (0.51 to 0.60) | 5.79E-51 | 3.84E-45 |
| HLA-DPB1 | DPB1*13:01 | 33 081 591 | 14 | 2.05 (1.82 to 2.31) | 6.10E-32 | 9.77E-30 |
| HLA-DQA1 | DQA1*04:01 | 32 640 529 | 14 | 1.86 (1.67 to 2.07) | 3.12E-29 | 2.97E-28 |
| HLA-DRB1 | DRB1*13:01 | 32 584 287 | 14 | 0.68 (0.62 to 0.75) | 2.15E-16 | 3.00E-14 |
| HLA-B | B*08:01 | 31 355 516 | 14 | 1.22 (1.15 to 1.30) | 1.29E-10 | 1.79E-12 |
| HLA-DQB1 | DQB1*05:01 | 32 663 284 | 14 | 1.20 (1.14 to 1.27) | 3.25E-10 | 1.33E-12 |
| HLA-DPB1 | DPB1*03:01 | 33 081 591 | 14 | 1.19 (1.12 to 1.27) | 3.15E-08 | 4.81E-08 |
| HLA-DPB1 | DPB1*06:01 | 33 081 591 | 13 | 1.47 (1.27 to 1.70) | 2.19E-07 | 2.15E-08 |
| HLA-DRB1 | AA Ile67 | 32 584 192 | 14 | 0.70 (0.67 to 0.73) | 1.70E-63 | – |
| HLA-DPB1 | AA Ile76 | 33 080 885 | 14 | 1.74 (1.56 to 1.93) | 1.73E-23 | 3.70E-29 |
| HLA-DRB1 | AA Tyr60 | 32 584 213 | 14 | 0.65 (0.62 to 0.69) | 3.50E-52 | 7.03E-22 |
| HLA-DQA1 | AA Thr69 | 32 641 502 | 14 | 1.85 (1.66 to 2.05) | 1.65E-30 | 1.90E-19 |
| HLA-DRB1 | AA Ala58 | 32 584 219 | 14 | 1.46 (1.37 to 1.55) | 2.88E-33 | 2.56E-14 |
| HLA-DPB1 | AA Leu11 | 33 080 690 | 14 | 1.21 (1.16 to 1.27) | 2.01E-16 | 1.65E-11 |
BP position based on build hg38.
Sequential conditional association analyses were performed separately for each variant type.
*Coding single-nucleotide polymorphisms: rs1126511 (SNP_DPB1_33156444), rs1142338 (SNP_DQA1_32717300) and rs1048372 (SNP_DQA1_32718414).
BP, base pair; N, number of cohorts where the variant was meta-analysed.