Colorectal cancer (CRC) is one of the most common cancers worldwide with a peak of incidence in industrialised countries. It is a complex disease related to environmental and genetic risk factors. Low-penetrance genetic variations contribute significantly to sporadic and familial form of CRC. Genome-wide association studies (GWAS) have uncovered numerous robust associations between common variants and CRC risk; only a few of those were protein altering non-synonymous polymorphisms. One of the hypotheses is that non-coding and intergenic variants may change the expression levels of one or several target genes and, thus, account for a fraction of phenotypic differences, including susceptibility to CRC. Such genetic variations have been detected as expression quantitative loci (eQTLs) that show linkage/association to a large number of genes and have been defined as "master regulators of transcription". In the present work, we overview the potentialities to use results from GWAS and eQTL studies in the identification as well as investigation of master regulators in CRC susceptibility.