Fig. 3: Interactions can lead to genotype-dependent and regulatory variant-set-dependent variance in a gene’s expression levels.

Simulated data illustrating that a gene A’s expression is only highest when the cis-eQTL genotype is 1/1 and the expression level of a distal gene (gene^B) is low. b Replotting the data in a on different axes illustrates how this interaction is associated with genotype-dependent variance in the expression of gene^A, with greater variance in expression between individuals when the eQTL genotype is 1/1. c The interaction leads to genotype-dependent differences in the slope of the relationship between gene^A and gene^B’s expression levels. d–f The same principle extended to sets of cis-regulatory variants. P-values derived from Spearman’s rho test.