Objective   To investigate the association of single nucleotide polymorphism (SNP) on chromosome 6q26-q27 with coronary artery disease (CAD).    Methods   A case-control association study of 165 identified unrelated CAD patients who admitted in our hospital from September 2008 to April 2010 and 166 matched normal controls from a Chinese Han population was performed. PCR-SSCP and nucleotide sequencing were used to genotype the SNP rs2048327-rs3127599-rs7767084-rs10755578 in SLC22A3-LPAL2-LPA gene.    Results   There were genotype AA and AG in CAD and control groups

but not GG in rs2048327

and the frequency of allele G was different between 2 groups (19.7% vs 11.1%

P=0.002). In rs3127599

genotype AG and GG was found in both groups

but no AA

and the frequency of allele A was different between 2 groups (7.6% vs 13.2%

P=0.017). Genotype CC

CT and TT in rs7767084 was found in both groups

and the frequency of allele C was different between 2 groups (16.4% vs 30.7%

P=0.000). Genotype CG and GG were seen in rs10755578 of both groups

but no CC was found

and the frequency of allele C was different between 2 groups (18.5% vs 12.7%

P=0.038). The frequencies of minor allele of the other SNPs were also significantly different after removing the confounding factors with logistical analysis except rs10755578. There was also statistical significance in the haplotype AGT

AGC

GGC and GGT between 2 groups (P0.05)

but not in the levels of TC

TG

HDL and LDL among different genotypes (P0.05).    Conclusion   Our findings suggest that the genetic polymorphisms in rs2048327-rs3127599-rs7767084 may be associated with the development of  CAD in Chinese Han population. The incidence rate of CAD in the crowd with haplotype AGT

GGC and GGT may be higher and there may be no association between genotype and the levels of TC

TG

HDL and LDL.