Fig. 1.

Definition of a cQTL. A cofactor is required for efficient transcription of a target gene by a TF. Polymorphism within the coding sequence of the cofactor gene or its promoter can change the expression or activity of the cofactor, which can influence the interaction between the cofactor and the TF and consequently the expression of the target gene. Thus, the “connectivity” between the TF and its target gene is influenced by the allelic identity at the cQTL. Variation in the activity of the TF is due to genetic variation at one or multiple trans-acting loci (aQTLs). The SNP within the cofactor gene is identified as a cQTL for the TF. The table shows how the variables are related.