The data are as follows: (1) methylation frequencies for the nine genes in sporadic and hereditary BC patients, (2) methylation frequencies of the same genes in the matched serum and methylation-positive BC tissues, (3) different methylation frequencies of HOXD13 and hMLH1 during the BC progression, (4) different methylation frequencies of HOXD13 and WNT5a between sporadic and hereditary BC, (5) DNA-methylated modification levels in different molecular subtypes of BC, and (6) ROC curve analysis of the three-gene methylation panel between BC, age-matched healthy and benign samples. Here, HOXD13 is linked to breast cancer.