Table 3.
Most significant secondary associations identified following conditioning on primary association signals
| Type | ID | Type | ID | Relative position | P-value | |
|---|---|---|---|---|---|---|
| SLE | SNP | rs1269852 | SNP | rs3135391 | Within HLA-DRA | 3.90E-06 |
| HLA | DRB1*1501 | 1.46E-05 | ||||
| UC | SNP | rs4639334 | SNP | rs382259 | NOTCH4 region | 4.82E-06 |
| HLA | DQB1*0502 | 4.82E-03 | ||||
| CD | SNP | rs382259 | SNP | rs4713436 | Within CDSN | 3.31E-04 |
| HLA | - | - | - | |||
| RA | HLA | DQA1*0301 | SNP | rs6457614 | Between HLA-DQA1 and HLA-DQA2 | 1.21E-17 |
| HLA | DQB1*0501 | 1.48E-21 | ||||
| MG | SNP | rs2523674 | SNP | - | - | - |
| HLA | - | - | - | |||
| IgAD | HLA | DQB1*0201 | SNP | rs3135352 | Between BTNL2 and HLA-DRA | 7.70E-07 |
| HLA | DRB1*1501 | 6.65E-07 | ||||
| MS | SNP | rs3135391 | SNP | rs2743951 | Between HLA-F and HLA-G | 1.88E-04 |
| HLA | HLA-B*4402 | 1.08E-08 |
Conditional logistic regression analysis was performed on each disease for the top HLA and top SNP. The top HLA and SNP signal following conditioning are shown for each of these alleles.