In this study, we demonstrated the presence of several genetic variations in regulatory elements, including promoters, enhancers, UTRs and introns, which might influence gene expression, as well as the functions, interactions and regulatory networks involving important genes, such as ATM/ATR, FGFR1, FOXA1, IGF1R, NF1, NOTCH2 and TOP2A, thus functionally impairing specific oncogenic signalling in breast cancer. The gene discussed is ATM; the disease is breast cancer.