The 3-dimensional organization of DNA inside of the nucleus impacts a variety of cellular processes, including gene regulation. Furthermore, it is apparent that somatic structural variants that affect how chromatin is organized in 3D can have a major impact on gene regulation and human disease. However, such structural variants in the context of cancer genomes are abundant, and predicting the consequence of any individual somatic mutation on 3D genome structure and gene expression is challenging. In addition, we are severely limited with regard to tools that can be used to study 3D folding of the genome in vivo in actual human tumor or tissue samples. Our lab has developed several approaches to address these challenges. We have taken a pan-cancer approach to identify loci in the genome that are affected by structural variants that alter 3D genome structure, and we have identified numerous loci with recurrent 3D genome altering mutations. We have also used genome engineering to create novel structural variants to better understand what types of mutations are actually capable of altering 3D genome structure and gene regulation. Finally, we have also developed novel tools to study 3D genome structure in vivo in complex tissue samples. We believe that these approaches will be critical for improving our understanding of how non-coding sequence variants can affect 3D genome structure and gene regulation, with the ultimate goal of understanding how these events affect human physiology.