Deep sequencing is enabling new insights into mechanisms of gene regulation including the involvement of intergenic elements. 97% of human DNA is non-coding, and significant portions of this comprise cis-regulatory elements such as enhancers, silencers or insulators which are involved in the spacial-temporal gene regulation. Recent whole genome sequencing as well genome-wide association studies have shown that alterations of these non-coding elements can modify specific signaling pathways and consequently lead to disease. However, in contrast to coding genes, there is no comprehensive record of such regions, making the investigation of regulatory elements alterations challenging. We are developing informatics solutions for integrating in-house and published high-throughput sequencing data (genome and epigenome) in order to decipher and annotate these unexplored segments of DNA. This will allow us to build a framework for the investigation of cancers genomic aberrations moving forward from coding genes, and identify non-coding alterations involved in tumorigenesis.