To investigate the association between rs12537 on 22q12.2 and breast cancer susceptibility as well as the clinical phenotype including familial history, menopausal status, estrogen receptor (ER), progestogen receptor (PR), human epidermal growth factor receptor 2 (HER-2) and molecular subtypes of breast cancer patients in Chinese Han population, we conducted a genotype-phenotype analysis to clarify the association of rs12537 with breast cancer phenotypes in Chinese Han population. This evidence concerns the gene ESR1 and breast cancer.