We next quantified the functional impact of SVs using expression quantitative trait loci (eQTL) associations as a surrogate34,35. Based on transcriptome data from lymphoblastoid cell lines derived from 462 individuals36 (the gEUVADIS consortium), we tested 18,969 expressed protein-coding genes for cis-eQTL associations, considering 1 Mbp candidate regions upstream and downstream of CDSs. A joint eQTL analysis using SNPs, indels and SVs with VAF >1% identified 54 eQTLs with a lead SV association (denoted SV-eQTL) and 9,537 eQTLs with a lead SNP/indel association (10% FDR). For an additional 166 eQTLs with lead associations to SNPs or indels, we observed SVs in LD (r2 > 0.5) seven times more than when using random variants matched for LD structure, distance to the transcription start site, and VAF, suggesting that a larger number of eQTLs are probably affected by SVs (Extended Data Fig. 8, Supplementary Table 7). In proportion to the number of variants tested, SV classes were up to ∼50-fold enriched for SV-eQTLs (P = 2.84 × 10−39, one-sided Fisher’s exact test; Supplementary Table 8). Large SVs were associated with increased effect size;
