To identify trans-eQTLs, we tested for association between every protein-coding or lincRNA gene and all autosomal variants where the gene and variant were on different chromosomes. To minimize false positives in trans-eQTL detection, we controlled for the same observed and inferred confounders as in the cis-eQTL analysis, and further removed genes with poor mappability, variants in repetitive regions, and trans-eQTLs between pairs of genomic loci with evidence of RNA-seq read cross-mapping due to sequence similarity. Applying this approach, we identified 673 trans-eQTLs at a 10% genome-wide FDR. This includes 112 distinct loci (R2 ≤ 0.2) and 93 unique genes (94 total gene associations, including a trans-eGene detected in both testis and thyroid) in 16 tissues (Extended Data Table 1, Extended Data Fig. 2b, Supplementary Information 7, 8, Supplementary Figs 12–15 and Supplementary Table 11). An alternative approach to quantifying FDR at the gene level (Supplementary Information 8 and Supplementary Table 12) identified 46 genes at 10% FDR, with estimated q values of less than 0.4 for all 94 gene associations identified using the genome-wide FDR16. By investigating long-range intra-chromosomal eQTLs
