Efforts are being directed to systematically analyze the non-coding regions of 
the genome for cancer-driving mutations1-6. cis-regulatory elements (CREs) 
represent a highly enriched subset of the non-coding regions of the genome in 
which to search for such mutations. Here we use high-throughput chromosome 
conformation capture techniques (Hi-C) for 19,023 promoter fragments to catalog 
the regulatory landscape of colorectal cancer in cell lines, mapping CREs and 
integrating these with whole-genome sequence and expression data from The Cancer 
Genome Atlas7,8. We identify a recurrently mutated CRE interacting with the ETV1 
promoter affecting gene expression. ETV1 expression influences cell viability 
and is associated with patient survival. We further refine our understanding of 
the regulatory effects of copy-number variations, showing that RASL11A is 
targeted by a previously identified enhancer amplification1. This study reveals 
new insights into the complex genetic alterations driving tumor development, 
providing a paradigm for employing chromosome conformation capture to decipher 
non-coding CREs relevant to cancer biology.