We investigated patterns of eQTL sharing using 22,286 genes (with RPKM > 0.1 in at least 10 samples) for each of the nine tissues with both a simple non–model-based analysis of every pair of tissues (22) and more sophisticated Bayesian models for joint analysis of all nine tissues (24, 25). Analyses focused on a ±100-kb window surrounding the TSS for each gene, which is smaller than used for the single-tissue analysis, as this is where we observe the highest eQTL density.
