The vast majority of top SNPs show a strong signal in at least one tissue (97% have a maximum |Z| score exceeding 4), consistent with most genes containing at least one eQTL in at least one tissue. However, in the tissue-by-tissue analysis ash identified only 13% of these effects as “significant” at lfsr < 0.05; that is, the univariate analysis was highly confident in the direction of the effect in only 13% of cases. By comparison, mash-bmalite identified 39% as significant at the same threshold, and mash identified 47%. Similar to our simulations, the significant associations identified by mash include the vast majority (95%) of those found by either of the other methods (Supplementary Table 4).
