These BC risk loci (together with coupled SNPs) are involved in amino acid modification of MMP9 protein (p.Q279R and p.574P, respectively), epigenetic control gene activity due to enhancer- and promoter-driven transcriptions in primary epithelial and myoepithelial breast cells, and gene expression/splicing level regulation in BC-related organs (brain, adipose, adrenal gland, thyroid, blood, etc.). This evidence concerns the gene MMP9 and breast cancer.