We found i) hypermethylation in EPCAM (17 CpG sites; p = 0.017) and RAD51C (27 CpG sites; p = 0.048); ii) hypermethylation in 36 CpG-specific sites (FDR q < 0.05) in the BC patients; iii) four specific CpG sites were associated with a higher risk of BC (FDR q < 0.01, Bonferroni p < 0.001): cg89786999-FANCI (OR = 1.65; 95% CI:1.2–2.2), cg23652916-PALB2 (OR = 2.83; 95% CI:1.7–4.7), cg47630224-MSH2 (OR = 4.17; 95% CI:2.1–8.5), and cg47596828-EPCAM (OR = 1.84; 95% CI:1.5–2.3). Here, MSH2 is linked to breast cancer.