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

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]