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Table 1 Major histocompatibility complex (MHC) associations to autoimmune diseases, as described by fine-mapping studies

From: The MHC locus and genetic susceptibility to autoimmune and infectious diseases

Disease Classic associated locus Fine-mapping: top locus HLA class for top association Fine-mapping: independent associations at P < 5 × 10–8 HLA class for independent association Population Sample size Reference
RA Shared epitope (HLA-DRB1 AA70-74) HLA-DRB1: AA 11, 13, 71, 74 II HLA-B AA 9 I European 5018 individuals with seropositive RA, 14,974 unaffected controls [19]
   HLA-DPB1 AA 9 II
HLA-DRB1: AA 11, 57, 74 II    Chinese, Korean 2782 seropositive RA cases, 4315 controls [34]
HLA-DRB1: AA 11, 71, 74 II HLA-DPB1 AA 84 II Japanese 6244 cases, 23,731 controls [25]
HLA-DOA (rs378352) II
HLA-B 40:02 I
CeD HLA DQ locus (DQ2, DQ8) HLA-DQA1: AA 25 and 47; HLA-DQB1: AA 57 and 74 II AA9 in HLA-DPβ1 II European 12,016 cases, 11,920 controls [35]
rs2301226 (near HLA-DPB1 gene) II
HLA-B*08:01 I
HLA-B*39:06 I
rs1611710 (HLA-F) I
Ps HLA-Cw6 (HLA-C 0602) HLA-C*06:02 I HLA-C*12:03 I European 9247 patients, 13,589 controls [36]
HLA-B amino acid 67 I
HLA-B amino acid 9 I
HLA-A amino acid position 95 I
HLA-DQα1 amino acid position 53 II
AS HLA-B27 HLA-B*27:02 and B*27:05 I HLA-A*02:01 I European 9069 AS cases, 13,578 controls [37]
HLA-DPB1 (rs1126513) II
HLA-DRB1*01:03 II
other HLA-B alleles (B*07:02) (protective), B*13:02, B*40:01, B*40:02, B*47:01, B*51:01 and B*57:01 (protective) I
SLE HLA-DRB1 (*03:01 and *15:01); TNF-308G/A; C4A null allele HLA-DRB1 AA 11, 12, 26 II HLA-DQB1*02 II Korean 849 SLE cases, 4493 controls [38]
HLA-DRB1*15:01-HLA-DQB1*06:02 II   
DRB1*0301 II rs419788 in intron 6 of the SKIV2L III European 314 trios [39]
rs1150753 in intronic region of TNXB III HLA-DRB1*03:01 II European 3701 cases, 12,110 controls [40]
HLA-DRB1*08:01 II
HLA-DQA1*01:02 II
rs8192591 (upstream of NOTCH4) III
rs2246618 near MICB I
HLA-DRB1 AA 13, 11; HLA-DRB1*15:01-HLA-DQB1*06:02 II    6 Asian cohorts (from China, Korea, Japan) 4478 cases, 12,656 controls [41]
T1D DRB1, DQB1, in particular heterozygosity for HLA-DR3/HLA-DR4 HLA-DQβ1 position 57; HLA-DRβ1 positions 13; HLA-DRβ1 positions 71 II HLA-B*39:06
HLA-B*18:01
HLA-B*50:01
HLA-DPB1*04:02
HLA-DPB1*01:01
HLA-A AA62
HLA-A*03
HLA-A*24:02
I
I
I
II
II
I
I
I
European 8095 cases, 10,737 controls [43]
DRB1, DQB1 II HLA-B*39
HLA-B*13
HLA-B*50
HLA-B*18
HLA-B*38 (protective)
HLA-A*24
I
I
I
I
I
I
European 2300 families [42]
MS HLA-DRB1*15:01 HLA-DRB1*15:01 II DRB1 alleles: *03:01, *13:03, *04:04, *04:01, and *14:01 II European 5091 cases, 9595 controls [45]
HLA-A*02:01 I
AA 65 of HLA-DPβ1 II
rs2516489 in MICB-LST1 locus III
HLA-B*37 I
HLA-DRB1*15:01 II HLA-DRB1*03:01, *13:03, *08:01 II European 17,465 cases, 30,385 controls [44]
HLA-DQB1*0302 II
HLA-A*02:01 (protective) I
HLA-B*44:02, *38:01, *55:01 (protective) I
CD HLA class II and HLA-C HLA-DRB1*01:03 II HLA-C*06:02 I European 18,405 cases, 34,241 controls [46]
UC HLA class II rs6927022(HLA-DQA1); HLA-DRB1*01:03 II HLA-C*12:02 I European 14,308 cases, 34,241 controls
Graves’ disease DRB1*03:01-DQA1*05:01-DQB1*02:01 (DR3-DQ2 haplotype), HLA-C HLA-DPB1 AA35, AA55, DPB1*05:01 II HLA-DPβ1 AA9 II Japanese 1956 cases, 7047 controls [24]
    HLA-A AA9 I
    HLA-B AA45, AA67 I
DM HLA-DPB1 HLA-DPB1*17 II HLA-DBP1 (rs7750458-A) II Han Chinese 127 cases, 1566 controls [47]
  1. RA rheumatoid arthritis, CeD celiac disease, Ps psoriasis, AS ankylosing spondylitis, SLE systemic lupus erythematosus, T1D type 1 diabetes, MS multiple sclerosis, CD Crohn’s disease, UC ulcerative colitis, DM dermatomyositis