α-Tthalassemia mental retardation X-linked (ATRX) is a chromatin remodeler frequently mutated in many cancers. Despite the binding pattern of ATRX in heterochromatin, ATRX-mediated epigenomic changes in cancer cells have not been profiled, especially for the heterochromatin regions. Here, we profiled genome-wide maps of chromatin accessibility in ATRX-intact and ATRX-null human cancer cells. We found extensive changes in chromatin accessibility in both repetitive DNA regions and non-repetitive regulatory regions following ATRX loss. These changes are highly correlated with changes in transcription, which lead to alterations in cancer-related signalling pathways, such as upregulation of the TGF-β pathway and downregulation of the cadherin family of proteins. These findings indicate that ATRX deficiency induces epigenomic changes and promotes tumorigenesis through both genome instability and shifts in transcription.