We identified multiple putative functional variants associated with transcriptional factors that have been found to be important for breast cancer, including GATA3, FOXA1, C/EBP, P300 and STAT3, and overlapped with binding motifs of transcriptional factors, including E2F3, C/EBP, HNF1B, PPARG and PAX. This evidence concerns the gene HNF1B and breast cancer.