We identified associations between the expression levels of all expressed genes (eGenes) and genetic variants (eVariants) located within 1 Mb of the target gene’s transcription start site (TSS), which we refer to as cis-eQTLs for convenience, without requiring evidence of allelic effects at each locus. However, the majority of cis-eQTLs do exhibit allele specific expression. We applied a linear model controlling for ancestry, sex, genotyping platform and latent factors12 in the expression data for each tissue that may reflect batch or other technical variables (see Methods; Extended Data Fig. 1, Supplementary Information 6 and Supplementary Figs 7–10). Considering all tissues, we found a total of 152,869 cis-eQTLs for 19,725 genes, representing 50.3% and 86.1% of all known autosomal long intergenic noncoding RNA (lincRNA) and protein-coding genes, respectively (Fig. 1a, b). We identified a median of 2,816 autosomal protein-coding or lincRNA 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
