Relationship between five GWAS-identified single nucleotide polymorphisms and female breast cancer in the Chinese Han population

With the development of genome-wide association study (GWAS), an increasing number of genetic variables have been confirmed to be associated with breast cancer. Furthermore, an increasing number of studies from Asian populations are becoming available. Few GWAS loci have been replicated in the Chinese Han population. In a case–control study of breast cancer in the Henan Tumor Hospital (253 cases/339 controls), we evaluated five SNPs from GWAS of populations of European or Asian ancestry. In order to evaluate the contribution of genetic factors to population differences in breast cancer subtypes, all cases are defined by estrogen (ER), progesterone (PR) receptor, Human epidermal growth factor receptor - 2 (HER2), and Ki67 status. Different genotypes of rs3803662 (TOX3)/ (TNRC9)) in the case group and the control group are statistically significant (P = 0.044), but the ones of rs10069690 (TERT), rs2046210 (6q25.1), rs2981582 (EGFR2), and rs889312 (MAP3K1) have no significant statistical differences with breast cancer (P = 0.772, 0.308, 0.376, 0.468). The allelic frequencies of rs3803662 between the case group and the control group differ in recessive genetic models (odds ratio (OR) = 2.04, 95 % confidence interval (CI) 1.14–3.66) and in con-dominant inheritance models (OR = 2.17, 95 % CI 1.18–4.00). Compared with AA and GA, GG increased the risk of breast cancer (P = 0.017, 0.013). The genotype of rs2046210 (6q25.1), rs2981582 (EGFR2), rs889312 (MAP3K1), and rs3803662 (TOX3/TNRC9) has no statistical differences in different subtypes of breast cancer. Five common breast cancer susceptibility loci from GWAS are not strongly associated with breast cancer risk among the Han Chinese of the Henan province; only rs3803662 (TOX3/TNRC9) is confirmed to increase the risk of breast cancer. The different genotypes of five loci distribute equally in different subtypes of breast cancer.