To understand the mechanism by which ZFX may regulate the cancer transcriptome, we performed ChIP-seq, NOMe-seq, and RNA-seq assays with knockdown experiments in HEK293T kidney, HCT116 colon, C4-2B prostate, and MCF-7 breast cancer cells, identifying ZFX-binding sites and ZFX-regulated genes throughout the human genome. This evidence concerns the gene ZFX and breast cancer.