Table 2.
Summary of Association Results and Conditioning Studies of HLA alleles in PBCa
| Marker/Amino Acid/HLA determinantb |
base pair position (HG19)c |
Allele 1 (Minor Allele)d |
Allele 2 | MAF (Case)e |
MAF (Control) |
p-valuef | Odds Ratio minor allele |
Cond. p- value DRB1g |
Cond. p- value DPB1g |
Cond. p- value DRB1 and DPB1g |
|---|---|---|---|---|---|---|---|---|---|---|
| rs115721871 | 32653792 | A | G | 0.17 | 0.08 | 9.8E-17 | 2.61 | 9.4E-02 | 1.3E-19 | 1.2E-01 |
| rs4246055 | 32592360 | C | T | 0.19 | 0.10 | 2.9E-16 | 2.47 | 2.1E-02 | 1.6E-19 | 2.8E-02 |
| rs114183935 | 32655730 | A | G | 0.59 | 0.43 | 8.1E-16 | 1.80 | 1.9E-02 | 1.2E-18 | 3.1E-02 |
| rs114432443 | 32652278 | T | C | 0.39 | 0.53 | 4.6E-15 | 0.55 | 2.3E-02 | 1.4E-17 | 2.8E-02 |
| rs116493712 | 32669767 | T | C | 0.57 | 0.46 | 1.1E-09 | 1.56 | 2.6E-01 | 5.2E-10 | 1.8E-01 |
| rs114796881 | 32664960 | A | G | 0.30 | 0.41 | 1.2E-09 | 0.63 | 3.9E-01 | 1.8E-10 | 3.7E-01 |
| rs114327274 | 32289594 | A | G | 0.24 | 0.17 | 4.1E-08 | 1.66 | 1.2E-01 | 1.9E-08 | 1.2E-01 |
| rs116348417 | 32389648 | A | G | 0.26 | 0.37 | 4.9E-08 | 0.66 | 5.2E-01 | 6.2E-11 | 5.7E-01 |
| HLA-DRB1*08 | 32552064 | SPEC | OTHER | 0.08 | 0.03 | 1.6E-11 | 3.22 | 1.0E+00 | 7.3E-13 | 1.0E+00 |
| HLA-DQB1*04:02 | 32631061 | SPEC | OTHER | 0.07 | 0.03 | 1.4E-10 | 3.16 | 6.8E-01 | 9.0E-12 | 4.5E-01 |
| HLA-DRB1*11 | 32552064 | SPEC | OTHER | 0.15 | 0.26 | 1.4E-10 | 0.55 | 1.0E+00 | 9.4E-13 | 8.3E-01 |
| HLA-DQA1*04:01 | 32608306 | SPEC | OTHER | 0.07 | 0.02 | 1.9E-10 | 0.32 | 6.5E-01 | 9.9E-12 | 5.0E-01 |
| HLA-DQB1*03:01 | 32631061 | SPEC | OTHER | 0.21 | 0.31 | 6.1E-09 | 0.61 | 8.9E-01 | 3.8E-10 | 4.5E-01 |
| HLA-DQB1*05:03 | 32631061 | SPEC | OTHER | 0.09 | 0.05 | 6.2E-07 | 2.14 | 7.6E-01 | 8.2E-09 | 1.0E+00 |
| HLA-DRB1*14 | 32552064 | SPEC | OTHER | 0.09 | 0.05 | 6.9E-07 | 2.12 | 1.0E+00 | 8.8E-09 | 1.0E+00 |
| HLA-DPB1*03:01 | 33049368 | DET | OTHER | 0.16 | 0.10 | 9.2E-07 | 1.78 | 4.2E-06 | 1.0E+00 | 1.0E+00 |
| DRB1-AA74 | 32551948 | OTHER | A | 0.43 | 0.31 | 1.2E-11 | 1.70 | 5.9E-01 | 3.2E-12 | 9.9E-01 |
| DRB1-AA74 | 32551948 | L | OTHER | 0.08 | 0.03 | 1.3E-11 | 3.23 | 2.9E-01 | 6.1E-13 | 2.0E-01 |
| DQA1-AA69 | 32609279 | T | OTHER | 0.08 | 0.03 | 2.7E-11 | 3.21 | 6.0E-01 | 8.5E-13 | 6.4E-01 |
| DRB1-AA58 | 32551996 | E | A | 0.15 | 0.26 | 1.5E-10 | 0.55 | 1.0E+00 | 9.4E-13 | 1.0E+00 |
This Table provides a summary of results before and after conditioning on particular HLA determinants and includes: 1) the top four imputed SNPs (rows 1–4); 2) top four genotyped SNPs (rows 5–8); 3) all classical HLA determinants with p-values < 10–6 (rows 9–16); and 4) the top four HLA amino acid (AA) associations (rows 17–20). P values after conditioning on particular HLA genes (see methods) are also shown. The p values were determined using SNPTEST V2 (see Patients and Methods) and used the genotype probabilities. A complete summary of strongly association markers is provided in Supplementary Table 1.
The SNP name, classical HLA determinant or AA is shown.
The position corresponding to the marker is shown (chromosomal base pair positions from HG19).
Allele 1 is the minor allele used for the analysis. For sequences designated with amino acid (AA) numbers the symbol refers to the allele symbol corresponds to standard AA nomenclature. Where the AA is compared with multiple other AAs, "Other" is used to represent all alternative AAs. The AA position includes the leader sequence (e.g. DRB1* position 104 is the same as AA position 74 without the leader sequence). Where HLA determinants are provided, the specificity is compared with not having the specificity (OTHER).
MAF: Minor allele frequencies were estimated from probabilities (SNPTEST V2).
p values before conditioning using population substructure and gender as covariates.
p value after conditioning on the allele(s) listed in the heading line.