Linkage disequilibrium structure of the 5q31-33 region in a Thai population.
A number of loci related to the immune response are located on human chromosomal region 5q31-33, and polymorphisms in this region have been reported to be associated with autoimmune and infectious diseases. In Southeast Asian populations, no systematic survey with dense SNP markers has been performed for the 5q31-33 region. In this study, the LD and haplotype structures for a 472-kb region on 5q31 were investigated in a Thai population to provide useful information for association studies. In addition, the LD structure in Thais was compared with that of the CHB and JPT HapMap populations (CHB + JPT) to evaluate the transferability of tagging SNPs from CHB + JPT for Thais. We show that the minor allele frequency, pattern of LD block, and genetic structure in the 5q31-33 region were highly concordant between Thais and CHB + JPT. A high transferability of tagging SNPs from CHB + JPT for Thais was observed. Our results suggest that tagging SNPs from CHB + JPT (Northeast Asians) can efficiently capture common variants in Southeast Asians, and that the HapMap data are useful for association studies in Southeast Asian populations.
Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.|Department of Medical Technology, Faculty of Allied Health Science, Naresuan University, Phitsanulok, Thailand.
Pornlada
P
Nuchnoi
Department of Human Genetics, Graduate School of Medicine, University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan. juno-tky@umin.ac.jp.
Jun
J
Ohashi
Department of Human Genetics, Graduate School of Medicine, University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan.
Izumi
I
Naka
Department of Parasitology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand.
Duangporn
D
Nacapunchai
Department of Human Genetics, Graduate School of Medicine, University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan.
Katsushi
K
Tokunaga
Department of Human Genetics, Graduate School of Medicine, University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan.
Nao
N
Nishida
Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
Jintana
J
Patarapotikul
D002874:Chromosome Mapping; D002895:Chromosomes, Human, Pair 5 / Q000737:chemistry; D030541:Databases, Genetic; D005787:Gene Frequency; D005828:Genetics, Population; D006801:Humans; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide; D016324:Sequence Tagged Sites; D013785:Thailand