note that this does not mean that the remaining 51.2% are all false positives. The false positive rate in the set of non-overlapping cis-eQTL signals depends on various unknown factors, which include the power to detect cis-eQTL signals of different strengths in both our data set and the comparison data set and, crucially, the proportion of eQTL signals in the human brain that remain undiscovered. If the latter proportion is large and the power of current studies is low, then two studies of equal power can both discover largely non-overlapping sets of true eQTL signals. This scenario is supported by the recent demonstration of large numbers of protein QTLs of small effect in yeast28.
