Fig. 2: Variant length influences the likelihood and effect size of eQTLs.

a Percentage of variants with length greater than the thresholds on the x axis that were eVariants (grey lines) or lead eVariants (green lines). Points are colored according to the enrichment (log 2 odds ratio) of variants above each threshold among eVariants or lead eVariants relative to variants smaller than the threshold; points circled in red were significant (FET two-sided, p < 0.05). A complete list of p values and odds ratios is provided in Supplementary Fig. 4. (b,c) Association of variant length with eQTL effect size for (b) non-exonic eQTLs or (c) exonic eQTLs mapped to biallelic deletions (n = 1,769 non-exonic, n = 48 exonic), duplications (n = 235 non-exonic, n = 13 exonic), multi-allelic CNVs (n = 1,278 non-exonic, n = 111 exonic) and STRs (n = 13,085 non-exonic, n = 148 exonic). Number of eQTLs for each variant class at defined length is shown in top panels. Points in bottom panels represent the centers of bins with equal numbers of observations and error bars indicate 95% confidence intervals around the mean (1000 bootstraps). Lines represent linear regressions, with 95% confidence intervals shaded, as calculated on unbinned data. p values at the right of each plot indicate the significance of the association between length and absolute effect size (linear regression, t-test) in a model that includes non-mode allele frequency and distance to TSS as covariates. p values presented are not adjusted for multiple testing.