title: A population-based LD map of the human chromosome 6p.
abstract: The recent publication of the complete sequence of human chromosome 6 provides a platform from which to investigate genomic sequence variation. We report here a detailed linkage disequilibrium (LD) pattern map across the entire human chromosome 6p by using a set of 1152 single nucleotide polymorphisms (SNPs) in a population of 198 Singaporean Chinese, with 326 SNPs focused in the major histocompatibility complex (MHC) region. Our analysis shows some unexpectedly high segments of strong LD in a 10-Mb region that includes the extremely polymorphic and gene-rich MHC loci and many non-MHC genes. These include the telomeric peri-MHC region that harbors olfactory receptors, histones and zinc finger clusters, and the centromeric peri-MHC region that contains several unknown open reading frames. The data also help refine a human-mouse synteny break in the region between 28.6 and 29.4 Mb. The population-based LD map presented here will provide an essential resource for understanding the genomic sequence variation of chromosome 6p and LD mapping of disease genes of complex genetic traits.
authors.affiliation: WHO Collaborating Center for Immunology, Faculty of Medicine, National University of Singapore.
authors.forename: Hong Xiang
authors.initials: HX
authors.lastname: Yu
authors.forename: Jer-Ming
authors.initials: JM
authors.lastname: Chia
authors.forename: Guillaume
authors.initials: G
authors.lastname: Bourque
authors.forename: Marie Vivien
authors.initials: MV
authors.lastname: Wong
authors.forename: Soh Ha
authors.initials: SH
authors.lastname: Chan
authors.forename: Ee Chee
authors.initials: EC
authors.lastname: Ren
mesh_terms: D002874:Chromosome Mapping; D002896:Chromosomes, Human, Pair 6; D006801:Humans; D015810:Linkage Disequilibrium; D008285:Major Histocompatibility Complex; D020641:Polymorphism, Single Nucleotide; D011995:Recombination, Genetic