Top genetic associations with MHC SNPs not previously characterised by GWAS
| Discovery set | Validation set | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Phenotype | ICD9 code | SNP | Position (bp,hg19) | Cases (MAF) | Controls (MAF) | Fisher's p value | OR (95% CI) | FDR | HLA haplotype (p value†) | Cases (MAF) | Controls (MAF) | Fisher's p value | OR (95% CI) | Meta-analysis p value |
| Unspecified histoplasmosis retinitis | 115.92 | rs3093983 | 31 496 925 | 12 (0.54) | 7406 (0.18) | 5.0E-05 | 5.3 (2.4 to 11.8) | 0.57 | HLA-DQB1 *06:02 (6.7E-4) | 8 (0.56) | 3879 (0.19) | 0.0005 | 5.7 (2.1 to 15.2) | 1.2E-07 |
| rs3093978 | 31 498 497 | 12 (0.54) | 7406 (0.18) | 5.0E-05 | 5.3 (2.4 to 11.8) | 0.57 | 8 (0.56) | 3879 (0.19) | 0.0005 | 5.6 (2.1 to 15.2) | 1.2E-07 | |||
| Haemangioma of intra-abdominal structures | 228.04 | rs3131003 | 31 093 482 | 31 (0.68) | 7387 (0.42) | 3.7E-05 | 2.9 (1.7 to 5.0) | 0.52 | HLA-C *12:03 (6.8E-4) | 25 (0.62) | 3862 (0.43) | 0.0078 | 2.2 (1.2 to 3.9) | 1.2E-06 |
| rs2523619 | 31 318 144 | 31 (0.45) | 7387 (0.20) | 5.1E-06 | 3.3 (2.0 to 5.5) | 0.23 | 25 (0.36) | 3862 (0.21) | 0.011 | 2.1 (1.2 to 3.8) | 2.7E-07 | |||
| Pneumonia due to Staphylococcus | 482.4 | rs3129234 | 33 111 347 | 15 (0.57) | 7403 (0.23) | 4.3E-05 | 4.4 (2.1 to 9.0) | 0.54 | HLA-DPB1 *03:01 (5.3E-4) | 6 (0.46) | 3881 (0.24) | 0.012 | 2.7 (1.2 to 6.0) | 2.1E-06 |
| rs3129214 | 33 117 258 | 15 (0.57) | 7403 (0.23) | 4.4E-05 | 4.4 (2.1 to 9.0) | 0.54 | 6 (0.46) | 3881 (0.24) | 0.022 | 2.7 (1.2 to 6.0) | 3.9E-06 | |||
| rs756440 | 33 122 331 | 15 (0.57) | 7403 (0.23) | 4.3E-05 | 4.4 (2.1 to 9.0) | 0.54 | 6 (0.46) | 3881 (0.24) | 0.011 | 2.7 (1.2 to 6.0) | 2.1E-06 | |||
| Lichen planus | 697.0 | rs12529049 | 32 357 715 | 97 (0.26) | 7321 (0.15) | 4.6E-05 | 2.0 (1.5 to 2.8) | 0.55 | HLA-DQB1 *05:01 (8.0E-08) | 81 (0.22) | 3806 (0.14) | 0.0032 | 1.8 (1.2 to 2.6) | 6.5E-07 |
| rs4248166 | 32 366 421 | 97 (0.30) | 7321 (0.18) | 1.4E-05 | 2.0 (1.5 to 2.8) | 0.38 | 81 (0.25) | 3806 (0.17) | 0.013 | 1.6 (1.1 to 2.3) | 8.3E-07 | |||
| rs13192471 | 32 671 103 | 97 (0.29) | 7321 (0.14) | 8.4E-08 | 2.5 (1.8 to 3.4) | 0.023 | 81 (0.23) | 3806 (0.14) | 0.0038 | 1.8 (1.2 to 2.6) | 1.9E-09 | |||
| rs1794275 | 32 671 248 | 97 (0.34) | 7321 (0.17) | 1.8E-08 | 2.5 (1.8 to 3.4) | 0.0071 | 81 (0.23) | 3806 (0.17) | 0.031 | 1.5 (1.0 to 2.2) | 3.3E-09 | |||
| rs2857106 | 32 787 570 | 97 (0.33) | 7321 (0.20) | 1.4E-05 | 2.0 (1.5 to 2.7) | 0.38 | 81 (0.28) | 3806 (0.19) | 0.0051 | 1.7 (1.2 to 2.4) | 3.4E-07 | |||
| Dyshidrosis | 705.81 | rs2844697 | 30 932 309 | 374 (0.43) | 7044 (0.35) | 1.2E-05 | 1.4 (1.2 to 1.6) | 0.34 | HLA-B *35:01 (0.0030) | 146 (0.41) | 3741 (0.35) | 0.042 | 1.3 (1.0 to 1.6) | 2.1E-06 |
| Other and unspecified nonspecific immunological findings | 795.79 | rs3094165 | 29 833 541 | 215 (0.23) | 7012 (0.32) | 2.6E-05 | 0.6 (0.5 to 0.8) | 0.47 | HLA-DRB1 *01:03 (0.0012) | 127 (0.26) | 3668 (0.32) | 0.044 | 0.7 (0.6 to 1.0) | 4.5E-06 |
| Infraspinatus (muscle) (tendon) sprain | 840.3 | rs13198118 | 30 770 732 | 10 (0.55) | 7408 (0.16) | 4.2E-05 | 6.4 (2.6 to 15.5) | 0.53 | HLA-DRB1 *08:10 0.0030 | 7 (0.36) | 3880 (0.16) | 0.034 | 3.0 (1.0 to 9.0) | 5.7E-06 |
| Contusion of wrist | 923.21 | rs9264942 | 31 274 380 | 264 (0.44) | 7154 (0.35) | 1.9E-05 | 1.5 (1.2 to 1.8) | 0.44 | HLA-C *03:03 (1.6E-4) | 98 (0.46) | 3789 (0.36) | 0.0076 | 1.5 (1.1 to 2.0) | 6.6E-07 |
†Reported are the haplotypes with minimum p values.
FDR, false discovery rate; GWAS, genome-wide association study; ICD9, International Classification of Disease V.9; MAF, minor allele frequency; MHC, major histocompatibility complex.