Six examples of SNPs that are associated with breast cancer susceptibility and predicted to affect TF binding and gene expression regulation.

Candidate SNPs are: 1) in strong LD (r2 ≥ 0.08) with the most associated breast cancer GWAS SNP; 2) within DNase/ATAC-seq defined regulatory region of MCF7, MCF10A, T47D, HMEC or vHMEC cell lines and tissue; 3) contain high information content (IC) in the TF binding PSWM (IC ≥ 0.5); and 4) are eQTLs in breast cancer patient solid tumor sample and GTEx breast tissue.候选单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点需满足以下全部条件：1) 与乳腺癌全基因组关联研究（Genome-Wide Association Study, GWAS）中关联性最强的单核苷酸多态性位点处于强连锁不平衡（Linkage Disequilibrium, LD）状态（r²≥0.08）；2) 位于MCF7、MCF10A、T47D、HMEC及vHMEC细胞系与组织的脱氧核糖核酸酶Ⅰ测序（DNase-seq）与转座酶可及性染色质测序（ATAC-seq）定义的调控区域内；3) 在转录因子结合位置权重矩阵（Position-Specific Weight Matrix, PSWM）中具有较高信息含量（Information Content, IC，IC≥0.5）；4) 在乳腺癌患者实体瘤样本及基因型-组织表达（Genotype-Tissue Expression, GTEx）数据库的乳腺组织中为表达数量性状位点（Expression Quantitative Trait Locus, eQTL）。