Extended HLA haplotype associations from factor analysis for whites
| Variant . | OR . | Control frequency . | Lower 95% CI . | Upper 95% CI . | FDR P . | Factor analysis . |
|---|---|---|---|---|---|---|
| A*26:01∼C*12:03∼B*38:01∼DRB4*01:01∼DRB1*04:02∼DQB1*03:02 | 2.05 | 0.0035 | 1.23 | 3.41 | 1.94E-04 | Group 1 |
| C*16:01∼B*44:03∼DRB4*01:01 | 0.79 | 0.0290 | 0.63 | 0.99 | 3.05E-02 | Group 2 |
| A*01:01∼C*07:01∼B*08:01∼DRB1*03:01∼DQB1*02:01 | 0.83 | 0.0636 | 0.70 | 0.99 | 2.07E-02 | Group 3 |
| DRB3*02:02∼DRB1*13:01∼DQB1*06:03 | 0.79 | 0.0401 | 0.65 | 0.96 | 6.79E-03 | Group 4 |
| B*52:01∼DRB5*01:02∼DRB1*15:02∼DQB1*06:01 | 1.54 | 0.0064 | 1.05 | 2.26 | 1.45E-02 | Group 5 |
| A*02∼C*03∼B*15 | 1.27 | 0.0280 | 1.01 | 1.58 | 2.13E-02 | Group 6 |
| DRBX*NNNN∼DRB1*01:01∼DQB1*05:01 | 0.84 | 0.0808 | 0.73 | 0.97 | 5.36E-03 | Group 7 |
| A*02∼C*03∼B*15∼DRB4*01∼DRB1*04∼DQB1*03 | 1.35 | 0.0142 | 1.02 | 1.78 | 2.55E-02 | Group 8 |
| C*02:02∼B*27:05∼DRB3*02:02 | 0.43 | 0.0047 | 0.20 | 0.92 | 1.59E-02 | Group 9 |
| C*02∼B*27∼DRB4*01∼DRB1*04∼DQB1*03 | 0.57 | 0.0071 | 0.34 | 0.95 | 2.25E-02 | Group 10 |
| C*03:04∼DRB4*01:01 | 1.18 | 0.0416 | 1.00 | 1.40 | 4.23E-02 | Group 11 |
| C*05:01∼B*44:02∼DRB1*11:01∼DQB1*03:01 | 0.48 | 0.0042 | 0.23 | 0.99 | 4.45E-02 | Group 12 |
| C*05:01∼B*44:02∼DRB1*13:01∼DQB1*06:03 | 0.62 | 0.0083 | 0.39 | 0.99 | 4.04E-02 | Group 13 |
| DRB3*03:01∼DRB1*13:02∼DQB1*06:04 | 0.82 | 0.0363 | 0.67 | 0.99 | 3.94E-02 | Group 14 |
| DRB5*01∼DRB1*15∼DQB1*05 | 4.80 | 0.0007 | 2.09 | 11.03 | 1.86E-06 | Group 15 |
| A*02:01∼DRB1*07:01 | 1.39 | 0.0314 | 1.13 | 1.70 | 9.57E-06 | Group 16 |
| C*01∼B*27∼DRBX*NN∼DRB1*01 | 0.62 | 0.0110 | 0.41 | 0.94 | 1.16E-02 | Group 17 |
| C*03∼B*15∼DRB4*01∼DRB1*04∼DQB1*03 | 1.37 | 0.0231 | 1.10 | 1.71 | 3.09E-04 | Group 18 |
| DRB3*02∼DRB1*11∼DQB1*03 | 0.89 | 0.1007 | 0.80 | 1.00 | 4.00E-02 | Group 19 |
| DRB4*01∼DRB1*04∼DQB1*02 | 2.02 | 0.0012 | 1.04 | 3.92 | 3.17E-02 | Group 20 |
| A*02:01 | 1.20 | 0.2670 | 1.08 | 1.34 | 3.29E-06 | Group 21 |
| C*03:03∼B*15:01∼DRB4*01:01 | 1.68 | 0.0057 | 1.11 | 2.52 | 2.39E-03 | Group 22 |
| C*12:03∼B*35:03 | 1.75 | 0.0027 | 1.06 | 2.86 | 1.78E-02 | Group 23 |
| C*07:01∼B*18:01 | 0.73 | 0.0216 | 0.56 | 0.95 | 8.97E-03 | Group 24 |
| C*01:02∼B*27:05∼DRBX*NNNN∼DRB1*01:01∼DQB1*05:01 | 0.60 | 0.0090 | 0.36 | 0.99 | 4.23E-02 | Group 25 |
| DRB4*01:01∼DRB1*07:01∼DQB1*03:03 | 1.49 | 0.0258 | 1.19 | 1.85 | 1.79E-07 | Group 26 |
| DRB3*02∼DRB1*11∼DQB1*06 | 8.14 | 0.0003 | 2.81 | 23.56 | 2.68E-08 | Group 27 |
| C*15:02∼B*51:01 | 0.73 | 0.0240 | 0.57 | 0.95 | 8.00E-03 | Group 28 |
| C*12:03 | 1.26 | 0.0473 | 1.07 | 1.50 | 4.73E-04 | Group 29 |
| A*02:01∼DRB1*14:01 | 1.71 | 0.0060 | 1.18 | 2.48 | 3.38E-04 | Group 30 |
| A*24:02∼C*07:01∼B*18:01 | 0.37 | 0.0040 | 0.14 | 0.94 | 2.52E-02 | Group 31 |
| C*12:03∼DRB4*01:01 | 1.63 | 0.0115 | 1.18 | 2.23 | 2.27E-05 | Group 32 |
| B*15∼DRB4*01∼DRB1*04∼DQB1*03 | 1.51 | 0.0090 | 1.08 | 2.11 | 3.66E-03 | Group 33 |
| DRB4*01:01∼DRB1*04:03 | 0.67 | 0.0100 | 0.46 | 0.99 | 4.53E-02 | Group 34 |
| DRB4*01∼DRB1*04∼DQB1*04 | 2.21 | 0.0015 | 1.17 | 4.18 | 6.80E-03 | Group 35 |
| DRB4*01:01∼DRB1*04:01∼DQB1*03:02 | 1.33 | 0.0383 | 1.12 | 1.58 | 1.86E-05 | Group 36 |
| C*03:04∼B*15:01∼DRB4*01:01 | 1.25 | 0.0191 | 1.01 | 1.54 | 4.01E-02 | Group 37 |
| DRB4*01:01∼DRB1*07:01 | 1.13 | 0.1322 | 1.01 | 1.27 | 1.46E-02 | Group 38 |
| C*16:02 | 1.83 | 0.0028 | 1.12 | 3.00 | 6.18E-03 | Group 39 |
| A*02∼B*14 | 1.55 | 0.0049 | 1.01 | 2.39 | 4.25E-02 | Group 40 |
| DQB1*06 | 0.91 | 0.2445 | 0.83 | 1.00 | 3.58E-02 | Group 41 |
| C*07∼B*44 | 1.33 | 0.0099 | 1.01 | 1.76 | 3.90E-02 | Group 42 |
| DRB1*15:01∼DQB1*06:03 | 12.90 | 0.0003 | 4.63 | 35.98 | 2.80E-14 | Group 43 |
| C*01∼B*15 | 2.66 | 0.0018 | 1.42 | 4.96 | 1.31E-05 | Group 44 |
| C*01:02∼DRB4*01:01 | 1.72 | 0.0047 | 1.10 | 2.69 | 4.58E-03 | Group 45 |
| C*04∼B*15 | 1.99 | 0.0025 | 1.16 | 3.41 | 3.06E-03 | Group 46 |
| A*02:05 | 1.37 | 0.0100 | 1.01 | 1.85 | 3.36E-02 | Group 47 |
| Variant . | OR . | Control frequency . | Lower 95% CI . | Upper 95% CI . | FDR P . | Factor analysis . |
|---|---|---|---|---|---|---|
| A*26:01∼C*12:03∼B*38:01∼DRB4*01:01∼DRB1*04:02∼DQB1*03:02 | 2.05 | 0.0035 | 1.23 | 3.41 | 1.94E-04 | Group 1 |
| C*16:01∼B*44:03∼DRB4*01:01 | 0.79 | 0.0290 | 0.63 | 0.99 | 3.05E-02 | Group 2 |
| A*01:01∼C*07:01∼B*08:01∼DRB1*03:01∼DQB1*02:01 | 0.83 | 0.0636 | 0.70 | 0.99 | 2.07E-02 | Group 3 |
| DRB3*02:02∼DRB1*13:01∼DQB1*06:03 | 0.79 | 0.0401 | 0.65 | 0.96 | 6.79E-03 | Group 4 |
| B*52:01∼DRB5*01:02∼DRB1*15:02∼DQB1*06:01 | 1.54 | 0.0064 | 1.05 | 2.26 | 1.45E-02 | Group 5 |
| A*02∼C*03∼B*15 | 1.27 | 0.0280 | 1.01 | 1.58 | 2.13E-02 | Group 6 |
| DRBX*NNNN∼DRB1*01:01∼DQB1*05:01 | 0.84 | 0.0808 | 0.73 | 0.97 | 5.36E-03 | Group 7 |
| A*02∼C*03∼B*15∼DRB4*01∼DRB1*04∼DQB1*03 | 1.35 | 0.0142 | 1.02 | 1.78 | 2.55E-02 | Group 8 |
| C*02:02∼B*27:05∼DRB3*02:02 | 0.43 | 0.0047 | 0.20 | 0.92 | 1.59E-02 | Group 9 |
| C*02∼B*27∼DRB4*01∼DRB1*04∼DQB1*03 | 0.57 | 0.0071 | 0.34 | 0.95 | 2.25E-02 | Group 10 |
| C*03:04∼DRB4*01:01 | 1.18 | 0.0416 | 1.00 | 1.40 | 4.23E-02 | Group 11 |
| C*05:01∼B*44:02∼DRB1*11:01∼DQB1*03:01 | 0.48 | 0.0042 | 0.23 | 0.99 | 4.45E-02 | Group 12 |
| C*05:01∼B*44:02∼DRB1*13:01∼DQB1*06:03 | 0.62 | 0.0083 | 0.39 | 0.99 | 4.04E-02 | Group 13 |
| DRB3*03:01∼DRB1*13:02∼DQB1*06:04 | 0.82 | 0.0363 | 0.67 | 0.99 | 3.94E-02 | Group 14 |
| DRB5*01∼DRB1*15∼DQB1*05 | 4.80 | 0.0007 | 2.09 | 11.03 | 1.86E-06 | Group 15 |
| A*02:01∼DRB1*07:01 | 1.39 | 0.0314 | 1.13 | 1.70 | 9.57E-06 | Group 16 |
| C*01∼B*27∼DRBX*NN∼DRB1*01 | 0.62 | 0.0110 | 0.41 | 0.94 | 1.16E-02 | Group 17 |
| C*03∼B*15∼DRB4*01∼DRB1*04∼DQB1*03 | 1.37 | 0.0231 | 1.10 | 1.71 | 3.09E-04 | Group 18 |
| DRB3*02∼DRB1*11∼DQB1*03 | 0.89 | 0.1007 | 0.80 | 1.00 | 4.00E-02 | Group 19 |
| DRB4*01∼DRB1*04∼DQB1*02 | 2.02 | 0.0012 | 1.04 | 3.92 | 3.17E-02 | Group 20 |
| A*02:01 | 1.20 | 0.2670 | 1.08 | 1.34 | 3.29E-06 | Group 21 |
| C*03:03∼B*15:01∼DRB4*01:01 | 1.68 | 0.0057 | 1.11 | 2.52 | 2.39E-03 | Group 22 |
| C*12:03∼B*35:03 | 1.75 | 0.0027 | 1.06 | 2.86 | 1.78E-02 | Group 23 |
| C*07:01∼B*18:01 | 0.73 | 0.0216 | 0.56 | 0.95 | 8.97E-03 | Group 24 |
| C*01:02∼B*27:05∼DRBX*NNNN∼DRB1*01:01∼DQB1*05:01 | 0.60 | 0.0090 | 0.36 | 0.99 | 4.23E-02 | Group 25 |
| DRB4*01:01∼DRB1*07:01∼DQB1*03:03 | 1.49 | 0.0258 | 1.19 | 1.85 | 1.79E-07 | Group 26 |
| DRB3*02∼DRB1*11∼DQB1*06 | 8.14 | 0.0003 | 2.81 | 23.56 | 2.68E-08 | Group 27 |
| C*15:02∼B*51:01 | 0.73 | 0.0240 | 0.57 | 0.95 | 8.00E-03 | Group 28 |
| C*12:03 | 1.26 | 0.0473 | 1.07 | 1.50 | 4.73E-04 | Group 29 |
| A*02:01∼DRB1*14:01 | 1.71 | 0.0060 | 1.18 | 2.48 | 3.38E-04 | Group 30 |
| A*24:02∼C*07:01∼B*18:01 | 0.37 | 0.0040 | 0.14 | 0.94 | 2.52E-02 | Group 31 |
| C*12:03∼DRB4*01:01 | 1.63 | 0.0115 | 1.18 | 2.23 | 2.27E-05 | Group 32 |
| B*15∼DRB4*01∼DRB1*04∼DQB1*03 | 1.51 | 0.0090 | 1.08 | 2.11 | 3.66E-03 | Group 33 |
| DRB4*01:01∼DRB1*04:03 | 0.67 | 0.0100 | 0.46 | 0.99 | 4.53E-02 | Group 34 |
| DRB4*01∼DRB1*04∼DQB1*04 | 2.21 | 0.0015 | 1.17 | 4.18 | 6.80E-03 | Group 35 |
| DRB4*01:01∼DRB1*04:01∼DQB1*03:02 | 1.33 | 0.0383 | 1.12 | 1.58 | 1.86E-05 | Group 36 |
| C*03:04∼B*15:01∼DRB4*01:01 | 1.25 | 0.0191 | 1.01 | 1.54 | 4.01E-02 | Group 37 |
| DRB4*01:01∼DRB1*07:01 | 1.13 | 0.1322 | 1.01 | 1.27 | 1.46E-02 | Group 38 |
| C*16:02 | 1.83 | 0.0028 | 1.12 | 3.00 | 6.18E-03 | Group 39 |
| A*02∼B*14 | 1.55 | 0.0049 | 1.01 | 2.39 | 4.25E-02 | Group 40 |
| DQB1*06 | 0.91 | 0.2445 | 0.83 | 1.00 | 3.58E-02 | Group 41 |
| C*07∼B*44 | 1.33 | 0.0099 | 1.01 | 1.76 | 3.90E-02 | Group 42 |
| DRB1*15:01∼DQB1*06:03 | 12.90 | 0.0003 | 4.63 | 35.98 | 2.80E-14 | Group 43 |
| C*01∼B*15 | 2.66 | 0.0018 | 1.42 | 4.96 | 1.31E-05 | Group 44 |
| C*01:02∼DRB4*01:01 | 1.72 | 0.0047 | 1.10 | 2.69 | 4.58E-03 | Group 45 |
| C*04∼B*15 | 1.99 | 0.0025 | 1.16 | 3.41 | 3.06E-03 | Group 46 |
| A*02:05 | 1.37 | 0.0100 | 1.01 | 1.85 | 3.36E-02 | Group 47 |
The longest extended haplotype association for each factor analysis group is listed. When multiple haplotypes had the same number of loci within the same factor analysis group, the most significant association is provided. When no haplotypes were contained in a factor analysis group, the most significant allelic association is provided. Lower 95% CI and upper 95% CI indicate the ORs for the 95% CI. FDR P value is the significance after FDR correction for multiple testing. A complete listing of allele and haplotype associations for each factor analysis group with additional information on uncorrected P values, case frequencies, and interactions for age, geography, and gender is provided in supplemental Table 1. CI, confidence interval.