vs. all transcripts and compared it with similar calculations for trans-SNPs associated with only one transcript at P< 5×10−8 (i.e. single-gene regulators). We find that the multi-gene regulators are enriched for greater number of true positives compared to single-gene regulators (Supplementary Fig. 10, Supplementary Table 9). We further investigated π1 values at trans-SNPs beyond our threshold of P< 5×10−8, and found that the median π1 increases with increasing significance of the top association per trans-SNP (Fig. 3B). As trans-SNPs with more significant association should be enriched for true positives, this confirms that a general property of true trans-SNPs might be regulation of multiple transcripts.
