We found that the overall tissue specificity of the eQTL sets varies. For example, eQTLs identified in skeletal muscle were less active in other tissues. Some tissues, such as brain, were not well captured by any of the nine eQTL sets here. ASE analysis also allows quantification of genome-wide tissue sharing of cis-regulatory signals without relying on eQTL discovery, but instead by measuring how often a site with a significant ASE signal in one tissue is significant in another tissue of the same individual. The proportion of shared ASE effects between tissue pairs within an individual varies between 36% and 58% (mean 46%), with slightly increased sharing observed between closely related tissues (conditioning on each site being measurable in both of the tissues) (fig. S22A). This relatively high degree of sharing is consistent with the eQTL results described above. If we relax the constraint of requiring a gene to be expressed in both tissues, then the proportion of shared ASE effects is substantially lower (0.85 to 39%, mean 11%; fig. S22B). This finding represents the total probability of detecting a
