title: Haplotype variation and linkage disequilibrium in 313 human genes.
abstract: Variation within genes has important implications for all biological traits. We identified 3899 single nucleotide polymorphisms (SNPs) that were present within 313 genes from 82 unrelated individuals of diverse ancestry, and we organized the SNPs into 4304 different haplotypes. Each gene had several variable SNPs and haplotypes that were present in all populations, as well as a number that were population-specific. Pairs of SNPs exhibited variability in the degree of linkage disequilibrium that was a function of their location within a gene, distance from each other, population distribution, and population frequency. Haplotypes generally had more information content (heterozygosity) than did individual SNPs. Our analysis of the pattern of variation strongly supports the recent expansion of the human population.
authors.affiliation: Genaissance Pharmaceuticals, Inc., Five Science Park, New Haven, CT 06511, USA. c.stephens@genaissance.com
authors.forename: J C
authors.initials: JC
authors.lastname: Stephens
authors.forename: J A
authors.initials: JA
authors.lastname: Schneider
authors.forename: D A
authors.initials: DA
authors.lastname: Tanguay
authors.forename: J
authors.initials: J
authors.lastname: Choi
authors.forename: T
authors.initials: T
authors.lastname: Acharya
authors.forename: S E
authors.initials: SE
authors.lastname: Stanley
authors.forename: R
authors.initials: R
authors.lastname: Jiang
authors.forename: C J
authors.initials: CJ
authors.lastname: Messer
authors.forename: A
authors.initials: A
authors.lastname: Chew
authors.forename: J H
authors.initials: JH
authors.lastname: Han
authors.forename: J
authors.initials: J
authors.lastname: Duan
authors.forename: J L
authors.initials: JL
authors.lastname: Carr
authors.forename: M S
authors.initials: MS
authors.lastname: Lee
authors.forename: B
authors.initials: B
authors.lastname: Koshy
authors.forename: A M
authors.initials: AM
authors.lastname: Kumar
authors.forename: G
authors.initials: G
authors.lastname: Zhang
authors.forename: W R
authors.initials: WR
authors.lastname: Newell
authors.forename: A
authors.initials: A
authors.lastname: Windemuth
authors.forename: C
authors.initials: C
authors.lastname: Xu
authors.forename: T S
authors.initials: TS
authors.lastname: Kalbfleisch
authors.forename: S L
authors.initials: SL
authors.lastname: Shaner
authors.forename: K
authors.initials: K
authors.lastname: Arnold
authors.forename: V
authors.initials: V
authors.lastname: Schulz
authors.forename: C M
authors.initials: CM
authors.lastname: Drysdale
authors.forename: K
authors.initials: K
authors.lastname: Nandabalan
authors.forename: R S
authors.initials: RS
authors.lastname: Judson
authors.forename: G
authors.initials: G
authors.lastname: Ruano
authors.forename: G F
authors.initials: GF
authors.lastname: Vovis
mesh_terms: D000483:Alleles; D000818:Animals; D044466:Asian People / Q000235:genetics; D044383:Black People / Q000235:genetics; D015226:Dinucleoside Phosphates / Q000235:genetics; D019143:Evolution, Molecular; D005260:Female; D014644:Genetic Variation; D006239:Haplotypes; D006579:Heterozygote; D006630:Hispanic or Latino / Q000235:genetics; D006801:Humans; D015810:Linkage Disequilibrium; D008297:Male; D009154:Mutation; D002679:Pan troglodytes / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D044465:White People / Q000235:genetics; D014960:X Chromosome / Q000235:genetics
chemical_list: D015226:Dinucleoside Phosphates; C015772:CpG dinucleotide