Genistein downregulated DNMT1, DNMT3B, DOT1L, UBE2A, AURKA, KDM1A, AURKB, KDM6B, HDAC5, HDAC1, SETD1B, SUV420H1, SUV39H1, HDAC6, DNMT3A, KDM5C and PAK1. Genistein also upregulated several chromatin modifiers including SETD5, SETD7, SETD6, CIITA and ESCO2. These genes could contribute to the anti-proliferative, anti-metastatic and anti-cancer activity of genistein. Here, HDAC1 is linked to cancer.