Table 4.
Conditioning on Specific HLA DRB1 and DPB1 Alleles
| Groupa | Marker/Amino Acid/HLA determinantb |
base pair position (HG19)c |
p-valued | Cond. p- value DRB1*08e |
Cond. p- value DRB1*11e |
Cond. p- value DRB1*14e |
Cond. p- value DPB1*03:01e |
|---|---|---|---|---|---|---|---|
| 1 | rs114991247 | 32583504 | 5.45E-13 | 2.41E-03 | 3.96E-13 | 2.15E-18 | 3.75E-14 |
| 1 | rs116240177 | 32561662 | 8.20E-13 | 4.82E-03 | 1.17E-12 | 3.66E-18 | 4.29E-14 |
| 1 | DRB1-AA74L | 32551948 | 1.33E-11 | 4.72E-01 | 2.26E-11 | 3.67E-16 | 1.48E-12 |
| 1 | HLA-DRB1*08 | 32552064 | 1.59E-11 | 1.00E+00 | 2.73E-11 | 4.55E-16 | 1.77E-12 |
| 1 | DQA1-AA69T | 32609279 | 2.75E-11 | 8.93E-01 | 3.55E-11 | 5.99E-16 | 2.35E-12 |
| 1 | HLA-DQB1*04:02 | 32631061 | 1.38E-10 | 5.79E-01 | 1.86E-10 | 4.02E-15 | 1.63E-11 |
| 1 | HLA-DQA1*04:01 | 32608306 | 1.90E-10 | 9.58E-01 | 1.73E-10 | 5.55E-15 | 2.01E-11 |
| 2 | rs9461776 | 32575735 | 3.02E-12 | 2.39E-14 | 3.35E-03 | 9.62E-15 | 1.53E-15 |
| 2 | rs115671039 | 32603212 | 1.98E-11 | 9.29E-13 | 4.62E-02 | 5.22E-13 | 2.91E-14 |
| 2 | HLA-DRB1*11 | 32552064 | 1.42E-10 | 1.34E-12 | 9.99E-01 | 4.34E-13 | 9.25E-14 |
| 2 | DRB1-AA58E | 32551996 | 1.45E-10 | 1.34E-12 | 9.98E-01 | 4.38E-13 | 9.30E-14 |
| 2 | DQB1-AA71T | 32632646 | 5.25E-10 | 3.65E-09 | 2.62E-04 | 4.68E-10 | 1.69E-12 |
| 2 | HLA-DQB1*03:01 | 32631061 | 6.10E-09 | 3.29E-10 | 9.76E-01 | 3.95E-10 | 3.25E-11 |
| 3 | rs380911 | 32209451 | 8.94E-09 | 1.36E-10 | 4.52E-06 | 3.71E-04 | 5.26E-09 |
| 3 | rs115240978 | 32672383 | 1.28E-08 | 1.30E-10 | 2.24E-06 | 6.75E-03 | 8.16E-10 |
| 3 | HLA-DQB1*05:03 | 32631061 | 6.21E-07 | 4.79E-09 | 5.13E-05 | 6.15E-01 | 2.31E-08 |
| 3 | HLA-DRB1*14 | 32552064 | 6.89E-07 | 5.29E-09 | 4.83E-05 | 9.99E-01 | 2.46E-08 |
| 3 | DRB1-AA57A | 32551999 | 6.90E-07 | 5.29E-09 | 4.82E-05 | 9.99E-01 | 2.46E-08 |
| 3 | DRB1-AA60H | 32551990 | 6.90E-07 | 5.29E-09 | 4.82E-05 | 9.99E-01 | 2.46E-08 |
| 4 | rs116751915 | 33052502 | 8.11E-09 | 9.21E-09 | 3.09E-06 | 1.76E-10 | 1.69E-04 |
| 4 | rs114761768 | 33050442 | 1.79E-08 | 3.09E-08 | 4.73E-06 | 4.90E-10 | 3.98E-04 |
| 4 | DPB1-AA76M | 33048662 | 6.13E-08 | 3.78E-07 | 2.11E-05 | 1.07E-08 | 8.71E-03 |
| 4 | DPB1-AA170I | 33052958 | 1.06E-07 | 2.61E-07 | 1.61E-05 | 3.21E-09 | 8.41E-03 |
| 4 | HLA-DPB1*03:01 | 33049368 | 9.18E-07 | 2.05E-06 | 1.01E-06 | 3.70E-09 | 9.98E-01 |
The group corresponds to those markers that are successfully controlled by specific HLA alleles (p value after conditioning is >1 × 10–4. The bold highlighted p-values indicate the p-values used in the “group” assignment. For each group the following are shown in this abbreviated summary: i) the two SNPs with the strongest association in the group; ii) the two HLA amino acids (AA) with the strongest association; and iii) all classical HLA alleles with p <10–6 prior to conditioning. The p values were determined using SNPTEST V2 (see methods) and used the genotype probabilities. A more complete summary of strongly association markers is provided in Supplementary Table 2.
The SNP name, classical HLA determinant or AA is shown. For the AA the letter following the residue number provides the relevant AA.
The position corresponding to the marker is shown (chromosomal base pair positions from HG19).
p values after conditioning using population substructure and gender as covariates.
p value after conditioning (Cond) on the allele(s) listed in the heading line.