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genetics  2012;44(11):1227-1230. PMCID: PMC3715052
 PMID: 23042117 Nature genetics  2012;44(3):291-296. The genetic
association of the major histocompatibility complex (MHC) to
rheumatoid arthritis risk has commonly been attributed to HLA-
DRB1 alleles. Yet controversy persists about the causal variants
in HLA-DRB1 and the presence of independent effects elsewhere in
the MHC. Using existing genome-wide SNP data in 5,018
seropositive cases and 14,974 controls, we imputed and tested
classical alleles and amino acid polymorphisms for HLA-A, B, C,
DPA1, DPB1, DQA1, DQB1, and DRB1 along with 3,117 SNPs across
the MHC. Conditional and haplotype analyses reveal that three
amino acid positions (11, 71 and 74) in HLA-DRβ1, and single
amino acid polymorphisms in HLA-B (position 9) and HLA-DPβ1
(position 9), all located in the peptide-binding grooves, almost
completely explain the MHC association