Quality control filtering and cis-trans search space reduction of Interactions in the pre-frontal cortex. Prior to main effect calculation, SNPs and the RNA probe sets underwent filtering for quality control. Cis- and trans-SNPs that had an independent effect on the abundance of RNA as measured on a micorarray were tested for epistatic effects on the abundance of that RNA. Only pairs of SNPs that were interchromosomal or not in linkage disequilibrium were considered. Additionally, for each of the nine genotypic combinations resulting from a pairwise interaction, only pairs that had a minimum sample size of ten individuals for each genotype were considered.