Upregulation of c-MYC in cis through a large chromatin loop linked to a cancer risk-associated single-nucleotide polymorphism in colorectal cancer cells.

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Published in Mol Cell Biol on January 11, 2010

Authors

Jason B Wright1, Seth J Brown, Michael D Cole

Author Affiliations

1: Department of Genetics, Dartmouth Medical School, Norris Cotton Cancer Center, Lebanon, NH 03756, USA.

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The myc oncogene: its role in transformation and differentiation. Annu Rev Genet (1986) 5.40

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Making myc. Curr Top Microbiol Immunol (2006) 1.87

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