Fine-scale SNP map of an 11-kb genomic region at 22q13.1 containing the galectin-1 gene.
Galectins, a family of animal lectins that bind beta-galactoside sugar chains, are thought to have a variety of intra- and extracellular functions. Through a case-control study in the Japanese population and subsequent functional analyses, we previously showed that a functional single nucleotide polymorphism (SNP) in the gene encoding galectin-2 (lectin, galactoside-binding, soluble, 2; LGALS2) is associated with susceptibility to myocardial infarction. As an addition to the genetic information about LGALS2 reported earlier, we provide here a map of polymorphic sites within an 11-kb region containing the gene encoding a closely related molecule, galectin-1 (lectin, galactoside-binding, soluble, 1; LGALS1). The map includes 14 SNPs and two genetic variations of other types detected in a Japanese population sample. Five of the 14 SNPs were not among those deposited in the dbSNP database in the US National Center for Biotechnology Information and appeared to be novel. We also analyzed linkage disequilibrium (LD) using the 12 SNPs in which minor-allele frequencies were >0.20. Investigation of haplotype structure within the LGALS1 locus revealed five common haplotypes covering more than 95% of the test population. One, or a pair, of the SNPs described here might serve as a "tag" for detecting associations between complex diseases and genes in this local segment of chromosome 22q13.1.
Iida
Aritoshi
A
Laboratory for Pharmacogenetics, Research Group of Personalized Medicine, RIKEN SNP Research Center, c/o RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan. iidaari@src.riken.go.jp.
Ozaki
Kouichi
K
Laboratory for Cardiovascular Diseases, RIKEN SNP Research Center, c/o Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
Tanaka
Toshihiro
T
Laboratory for Cardiovascular Diseases, RIKEN SNP Research Center, c/o Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
Nakamura
Yusuke
Y
Laboratory for Pharmacogenetics, Research Group of Personalized Medicine, RIKEN SNP Research Center, c/o RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.|Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
D000483:Alleles; D001483:Base Sequence; D002874:Chromosome Mapping; D002892:Chromosomes, Human, Pair 22 / Q000235:genetics*; D004247:DNA / Q000235:genetics; D037483:Galectin 1 / Q000235:genetics*; D005787:Gene Frequency; D005838:Genotype; D006801:Humans; D007564:Japan; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide
D037483:Galectin 1; D004247:DNA