measure of the proportion of the heritability that is explained by variants in cis. Next, each gene’s expression value was corrected by the cis-eQTL effects and calculated as the residuals of the linear regression of the original gene expression levels on the independent cis-eQTL for each gene. The global regression procedure was then repeated but, in this case, using the gene expression values corrected by the common cis-eQTL effects. The coefficient of this regression represented the estimate of the average gene expression variance explained by variants not discovered in our eQTL analysis, most likely rare variants. Subtracting this value from the total heritability in cis, an estimate of the genetic variance at the cis-regions that is due to common SNPs was obtained. All three tissues were analyzed separately and linear regressions were adjusted using the software R version 2.13.0 37.
