We identified four breast cancer risk-related genes that are differentially methylated in both site-specific and DMR analyses (LHX2, TFAP2B, JAKMIP1, and SEPT9) in the main analysis of normal breast tissue, and three genes overlapping the main analysis and two independent datasets of normal breast tissue and blood (POM121L2, KCNQ1, and CLEC4C). This evidence concerns the gene LHX2 and breast cancer.