Genetic variants of haplotypes in the 5′-flanking region of protein phosphatase 2A-Aα gene in Cantonese,China

Objective To investigate the linkage disequilibrium(LD) and haplotype distribution of genetic variants in the 5′-flanking region of PP2A-Aα subunit gene(PPP2R1A) in Guangdong Han population.Methods HaploView software was used to analyze the genetic characteristics,the LD and the tag of seven single nucleotide polymorphisms(SNP) previously identified by DNA sequencing in the 5′-flanking region of PPP2R1A.Results All the allele frequencies were in the Hardy-Weinberg equilibrium(P0.05).The population heterozygosities(π) of 6 SNPs were over 0.15,while a novel-512GA SNP site was 0.05.The results showed that these polymorphisms had high LD between-1039GT and +87TC,-1039GT and +108AG,-568GA and-241-/G in the population.Complete LD was found between +87TC and +108AG.Five major haplotypes were established,while wild type haplotype was 53%.Tag SNPs were confirmed for four polymorphisms,including-1039GT(+Ins),-512GA,-241-/G and +107-/C.Two haplotype blocks were constructed,and their representative haplotypes were constructed with-512GA and +108AG as haplotype tag SNP(htSNP).Conclusion The tag SNPs and the haplotypes of genovariants in 5′-flanking region of PPP2R1A were identified for general Guangdong Han Chinese population.These results provide a basis for the further functional analysis of promoter haplotypes.