eGenes at a 5% false discovery rate (FDR) within each tissue (Extended Data Fig. 2a). Protein-coding genes without a cis-eQTL in any tissue were more likely to be expressed at low levels or loss-of-function intolerant and were enriched for functions related to development and environmental response, indicating specific contexts in which additional eQTLs may be identified (Extended Data Fig. 3). To identify cis-eGenes affected by more than one functional regulatory variant, we applied forward–backward stepwise regression (see Methods). This approach identified an additional 24,886 secondary cis-eQTLs, with 41.2% of protein-coding genes and 24.8% of lincRNAs having multiple, conditionally independent eVariants in at least one tissue (Supplementary Fig. 11).
