A population-based LD map of the human chromosome 6p.
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.
Yu
Hong Xiang
HX
WHO Collaborating Center for Immunology, Faculty of Medicine, National University of Singapore.
Chia
Jer-Ming
JM
Bourque
Guillaume
G
Wong
Marie Vivien
MV
Chan
Soh Ha
SH
Ren
Ee Chee
EC
D002874:Chromosome Mapping; D002896:Chromosomes, Human, Pair 6; D006801:Humans; D015810:Linkage Disequilibrium; D008285:Major Histocompatibility Complex; D020641:Polymorphism, Single Nucleotide; D011995:Recombination, Genetic