AimTakayasu arteritis (TA) is a rare autoimmune disease with ethnic differences. Genome-wide association studies (GWAS) showed novel genetic variants in the human leukocyte antigen (HLA) region were associated with TA. The present study aimed to investigate the linkage between these single nucleotide polymorphisms (SNP) and TA in a Chinese Han population. MethodsFour hundred and twelve patients from multiple centers and 597 healthy controls were genotyped using the Sequenom MassArray iPLEX platform. The association between these SNPs and various clinical symptom of TA was also investigated. ResultsOur study showed a higher risk allele frequency of rs12524487 in TA patients compared to healthy controls (26.6% vs. 21.7%, odds ratio [OR] 1.31, 95% CI 1.06-1.61). The other SNP rs9366782 in HLA-B/MICA (major histocompatibility complex class I polypeptide-related sequence A) showed association with TA ischemic brain disease (OR: 1.78, 95% CI: 1.16-2.73, P-c = 0.03). However, rs3763288 and rs114202986 in MICA were negatively related to TA either as a whole or in any clinical features. Meanwhile, ATGT(rs9366782, rs12524487, rs3763288 and rs114202986) were the risk haplotypes (P-c = 2.48 x 10(-10)). ConclusionsOur findings indicated that rs12524487 in HLA-B/MICA was a genetic risk factor for TA in a Chinese Han population and rs9366782 in this region was associated with ischemic brain disease in TA but not TA susceptibility.