Disentangling genetic effects on transcriptional and post-transcriptional gene regulation through integrating exon and intron expression QTLs.

Nevertheless, we found a small but significant bias towards top ex-inQTL signals being more frequently shared with secondary exQTL and inQTL signals (5.4% and 8.8%, respectively) than the opposite (top exQTL or top inQTL signals shared with secondary ex-inQTL signals: 3.5% and 6.7%; p < 0.05, Fisher’s exact test; Supplementary Fig. 3D ).

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We mapped cis-QTL with QTLtools 1.3 39 to obtain (1) the top cis-QTL association for each gene after empirically adjusting p values using 1000 permutations, (2) all nominally significant associations, and (3) conditional cis-QTL associations after stepwise regressing out stronger, masking cis-QTL signals from the gene expression measurements.

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