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; for example, a twofold increase in effect size for genic SVs >10 kbp versus variants <1 kbp (P = 0.0004; t-test; Extended Data Fig. 8). Taken together, although SNPs contribute more eQTLs overall, our results suggest that SVs have a disproportionate impact on gene expression relative to their number.
