Table 1.
Haplotypes defined by HlA-DQβ1 position 57, HlA-DRβ1 position 13 and HlA-DRβ1 position 71 (control frequency > 0.1%)
| Haplotype | OR | Control freq. | Case freq. | Classical HLA-DQB1 alleles | Classical HLA-DRB1 alleles |
|---|---|---|---|---|---|
| A-H-K | 2.13 | 0.050 | 0.248 | 0201, 0202, 0302, 0304, 0305 | 0401, 0409 |
| A-H-E | 1.33 | 0.005 | 0.016 | 0201, 0202, 0302, 0304, 0305 | 0402, 0437 |
| A-S-K (ref) | 1.00 | 0.145 | 0.332 | 0201, 0202, 0302, 0304, 0305 | 0301, 0302, 0304, 1303 |
| A-H-R | 0.89 | 0.054 | 0.107 | 0201, 0202, 0302, 0304, 0305 | 0403, 0404, 0405, 0406, 0407, 0408, 0410, 0411 |
| A-S-E | 0.53 | 0.001 | 0.001 | 0201, 0202, 0302, 0304, 0305 | 1102, 1103, 1301, 1302, 1304 |
| D-F-R | 0.48 | 0.012 | 0.014 | 0301, 0303, 0401, 0402, 0503, 0601, 0602, 0603 | 0101, 0102, 0901, 1001 |
| A-F-R | 0.43 | 0.001 | 0.001 | 0201, 0202, 0302, 0304, 0305 | 0101, 0102, 0901, 1001 |
| S-R-R | 0.37 | 0.008 | 0.007 | 0502, 0504 | 1601, 1602 |
| V-F-R | 0.35 | 0.106 | 0.085 | 0501, 0604, 0609 | 0101, 0102, 0901, 1001 |
| V-S-E | 0.34 | 0.040 | 0.030 | 0501, 0604, 0609 | 1102, 1103, 1301, 1302, 1304 |
| D-G-R | 0.32 | 0.039 | 0.029 | 0301, 0303, 0401, 0402, 0503, 0601, 0602, 0603 | 0801–0806, 1201, 1202, 1404, 1415 |
| D-H-K | 0.27 | 0.068 | 0.042 | 0301, 0303, 0401, 0402, 0503, 0601, 0602, 0603 | 0401, 0409 |
| V-F-E | 0.24 | 0.013 | 0.006 | 0501, 0604, 0609 | 0103 |
| A-Y-R | 0.18 | 0.103 | 0.043 | 0201, 0202, 0302, 0304, 0305 | 0701 |
| D-S-E | 0.11 | 0.058 | 0.015 | 0301, 0303, 0401, 0402, 0503, 0601, 0602, 0603 | 1102, 1103, 1301, 1302, 1304 |
| D-F-E | 0.08 | 0.004 | 0.001 | 0301, 0303, 0401, 0402, 0503, 0601, 0602, 0603 | 0103 |
| D-H-R | 0.06 | 0.017 | 0.002 | 0301, 0303, 0401, 0402, 0503, 0601, 0602, 0603 | 0403–0408, 0410, 0411 |
| D-S-K | 0.06 | 0.010 | 0.001 | 0301, 0303, 0401, 0402, 0503, 0601, 0602, 0603 | 0301, 0302, 0304, 1303 |
| D-S-R | 0.05 | 0.083 | 0.010 | 0301, 0303, 0401, 0402, 0503, 0601, 0602, 0603 | 1101, 1104, 1106, 1108, 1305, 1401, 1402, 1405, 1406, 1407 |
| D-Y-R | 0.03 | 0.041 | 0.003 | 0301, 0303, 0401, 0402, 0503, 0601, 0602, 0603 | 0701 |
| D-R-A | 0.02 | 0.140 | 0.005 | 0301, 0303, 0401, 0402, 0503, 0601, 0602, 0603 | 1501 |
The 3 amino acid positions define 21 common haplotypes. We list their multivariate ORs and frequencies in controls and cases, as well as the classical four-digit alleles tagged by each haplotype. See Supplementary Table 5b for multivariate ORs and P values for all 31 haplotypes formed by HLA-DQβ1 position 57, HLA-DRβ1 position 13 and HLA-DRβ1 position 71. Freq., frequency.