HLA and SNP haplotype mapping in the Japanese population

H. Kitajima, M. Sonoda, K. Yamamoto

Research output: Contribution to journalArticlepeer-review

9 Citations (Scopus)


The genes that encode the human leukocyte antigen (HLA) class I and II molecules are highly polymorphic and located in the major histocompatibility complex (MHC) region, where there is a high density of immune-related genes. Numerous studies have identified disease susceptibility in this region; however, interpretation of the results is complicated because of the strong linkage disequilibrium (LD) among HLA alleles and single-nucleotide polymorphisms (SNPs). In this study, we evaluated the correlation between the HLA alleles of 6 loci (HLA-A, C, B, DRB1, DQB1 and DPB1) and 6502 SNPs within 8 Mb of the extended MHC region using 92 Japanese subjects to identify SNP single loci or haplotypes that tag HLA alleles. We found a total of 39 HLA alleles that showed strong LD (r2≥0.8) with SNPs, including 11 non-synonymous SNPs in non-HLA genes. In addition, we identified several SNP haplotypes in strong LD (r2≥0.8) with eight HLA alleles, which do not possess tag SNPs. Our detailed list of tag SNPs and haplotypes could be utilized for a better understanding of the results obtained by association studies in the Japanese population and for the characterization of the differences in LD structures between races.

Original languageEnglish
Pages (from-to)543-548
Number of pages6
JournalGenes and Immunity
Issue number7
Publication statusPublished - 2012 Oct
Externally publishedYes


  • HLA
  • disease susceptibility
  • linkage disequilibrium
  • tag SNP
  • tag SNP haplotype

ASJC Scopus subject areas

  • Immunology
  • Genetics
  • Genetics(clinical)


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