The absence of interaction effects is readily visualized by plotting expression as a function of genotype with color coding of each location, for each association. An example of a trans association in Supplementary Figure 9 online shows the clear trend of increased expression of AMY1A (chromosome 1) in homozygotes for the A allele of ACTG1 gamma actin (chromosome 17), consistently across the three locations despite slight overall location effects. Expression of AMY1A is highly correlated with that of AMY1B (r > 0.8) as well as of dozens of other genes in a co-expression module, but the eSNP only regulates AMY1A, because it increases expression of the gene two-fold in an additive manner. A similar plot for a representative gene that shows highly significant location and genotype effects in cis, C21ORF57, is provided in Figure 6a and further discussed below, and further examples can be seen in Supplementary Figure 9c online.
