Of greater interest is that we also found a subset of eQTLs that appear to be tissue specific, despite the probes being reliably detected in all samples series. It is possible that genetic variants can affect expression levels exclusively in a subset of tissues. For example, gene expression may be altered in a tissue- and timing-specific manner by cis-regulatory elements (Cooper et al., 2008). In this case, although multiple tissues may be permissive for expression, different -cis regulatory elements are being employed in each tissue and lead to quantitatively different expression levels. Understanding why there are examples where differences in expression do not explain eQTL detection in a simple way will be an important question for future studies.
