A haplotype map of the extended human MHC

Identification of susceptibility loci in infectious and autoimmune diseases is challenging due to linkage disequilibrium that extends across the major histocompatibility complex in the human genome. The extended MHC is a region of around 8-Mb on chromosome 6 containing over 250 protein-coding genes. Recently, an international consortium of researchers created a resource to characterize the LD patterns between the highly polymorphic HLA genes and background variation by typing the classical HLA genes and >7,500 common SNPs and deletion-insertion polymorphisms across four population samples.

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  • Phased haplotypes: YRI | CEU+ | CHB | JPT (PHASE format, original files from Jonathan Marchini)
  • Marker information: YRI | CEU+ | CHB | JPT (original files from Jonathan Marchini)
    All positions are relative to NCBI build 34.
  • Phased haplotypes: YRI | CEU+ | CHB | JPT
    These files are in Nick Patterson format. Alleles for the SNPs are coded as 1=A, 2=C, 3=G, 4=T. HLA alleles are down-coded as multiple binary alleles where 0=absent, 1=present.
  • Marker information: YRI | CEU+ | CHB | JPT
    All positions are relative to NCBI build 34.
  • Phased haplotypes: YRI | CEU+ | CHB | JPT (no allele down-coding, and with CEPH sample IDs)
  • List of tags for HLA alleles: Supplementary Table 3 from de Bakker et al.

Links

Reference

P.I.W. de Bakker, G. McVean, P.C. Sabeti, M.M. Miretti, T. Green, J. Marchini, X. Ke, A.J. Monsuur, P. Whittaker, M. Delgado, J. Morrison, A. Richardson, E.C. Walsh, X. Gao, L. Galver, J. Hart, D.A. Hafler, M. Pericak-Vance, J.A. Todd, M.J. Daly, J. Trowsdale, C. Wijmenga, T.J. Vyse, S. Beck, S.S. Murray, M. Carrington, S. Gregory, P. Deloukas, J.D. Rioux (2006) A high resolution HLA and SNP haplotype map for disease association studies in the extended human MHC. Nature Genetics. 38: 1166-1172