HLA-DQβ1 amino acid position 87 and DQB1*0301 are associated with Chinese Han SLE.

BackgroundSeveral susceptibility loci have been identified associated with Chinese Han systemic lupus erythematosus (SLE). MethodsWe carried out imputation of classical HLA alleles, amino acids and Single Nucleotide Polymorphisms (SNPs) across the MHC region in Chinese Han SLE genome-wide association study (GWAS) of mainland and Hong Kong populations for the first time using newly constructed Han-MHC reference panel followed by stepwise conditional analysis. ResultsWe mapped the most significant independent association to HLA-DQ1 at amino acid position (Phe87, p=7.807x10(-17)) and an independent association at HLA-DQB1*0301 (P-condiational=1.43x10(-7)). ConclusionOur study illustrates the value of population-specific HLA reference panel for fine-mapping causal variants in the MHC.