Research on mA-associated SNPs (mA-SNPs) has emerged recently due to their possible critical roles in many key biological processes. In this sense, several investigations have identified mA-SNPs in different diseases. In order to gain a more complete understanding of the role that mA-SNPs can play in breast cancer, we performed an analysis to identify the mA-SNPs associated with breast cancer and to evaluate their possible effects. For this purpose, we downloaded SNPs related to breast cancer and a list of mA-SNPs from public databases in order to identify which ones appear in both. Subsequently, we assessed the identified mA-SNPs by expression quantitative trait loci (eQTL) analysis and differential gene expression analysis. We genotyped the mA-SNPs found in the analysis in 35 patients with breast cancer, and we carried out a gene expression analysis experimentally on those that showed differences. Our results identified 981 mA-SNPs related to breast cancer. Four mA-SNPs showed an eQTL effect and only three were in genes that presented an altered gene expression. When the three mA-SNPs were evaluated in the tissue sample of our breast cancer patients, only the mA-SNP rs76563149 located in gene presented differences in allele frequencies and a low gene expression in breast cancer tissues, especially in luminal B HER2+ subtype. Future investigations of these mA-SNPs should expand the study in different ethnic groups and increase the sample sizes to test their association with breast cancer and elucidate their molecular function.