Linkage disequilibrium and haplotypes in 5′-flanking region of the human protein phosphatase 2A-Bδ gene in the Cantonese

Objective To investigate the linkage disequilibrium and distribution of haplotypes in the promoter region of PP2A-Bδ subunit gene(PPP2R2D) in population.Methods polymorphisms,-1684AG(rs11146169),-1196CT(rs9419202),-462GA(rs7074421) and-1610AT,identified by DNA resequencing in 5′-flanking region of PPP2R2D in our previous study,were analyzed with HaploView software and chi-square test for the analysis of genetic index,linkage disequilibrium(LD),tag SNP and haplotype in 50 healthy Cantonese excluded acute or chronic disease by check-up. Results The genotype frequencies of four single polymorphisms were in the Hardy-Weinberg equilibrium(P0.05).The population heterozygosities(π) of each polymorphism were-1684 AG(0.020),-1610 AT(0.132),-1196CT(0.059) and-462 GA(0.059),respectively.There was no variant homozygous genotyping.The heterozygosity of-1196CT and-462 GA were significantly low in this population compared with HapMap-CEU and –YRI population(P0.05).The polymorphisms were in complete LD for-1196 CT and-462 GA in our studied population.Three major haplotypes(H1-H3) in 5′-flanking region of PPP2R2D were constructed.The frequency of wild type haplotype(H1) was 89.0% in current population,and that of two variant haplotypes were 7.0% in H2 and 3.0% in H3.Three polymorphisms determined as tag SNPs were-1684 AG,-1610 AT and-462 GA.Conclusion The tag SNPs and haplotypes in 5′-flanking region of PPP2R2D were firstly identified and reported in the Han Nationality in Guangdong of South China.These results provided the basis for the further functional analysis of these polymorphism haplotypes.