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Associations between “lipid-related” candidate genes,blood lipid concentrations and coronary artery disease (CHD) risk are not clear.We aimed to investigate the effect of three newly identified lipids loci from genome-wide association studies on CHD and blood lipid levels in Chinese Han population.The genotypes of SNPs at three newly identified lipid loci and blood lipids concentrations were examined in 1360 CHD patients and 1360 age- and sex-frequency matched controls from an unrelated Chinese Han population.Allele T of rs16996148 occurred less frequently in CHD patients with the odds ratio (OR) being 0.64 (95％ CI 0.50 to 0.81),after adjusting for conventional risk factors and was associated with a 33％ decreased CHD risk (P＜0.01) comparing with the major allele G.Individuals with GT genotype had the lowest CHD risk.No associations were found between the polymorphisms of other two loci with CHD risk and all three SNPs had no effect on lipid profile in this population.SNP rs16996148 on chromosome 19p13 is significantly associated with lower risk for CHD in Chinese Han population.However,it remains unresolved why these lipid-related loci had significantly less effects than the correspondingly expected effects on blood lipids levels in this population.