The non–model-based pairwise analysis method identifies significant SNP-gene pairs in a first tissue, and then uses the distribution of the P values for these pairs in the second tissue to estimate π1, the proportion of non-null associations in the second tissue (22, 26). Estimated values of π1 ranged from 0.54 to 0.90 (Fig. 2B). For every pair of tissues, we observed a high level of sharing of eQTLs, and this pairwise sharing of eQTL among tissues roughly mirrored the tissue gene expression correlations (fig. S12).
