Fig. 3: Properties of SV and STR eQTLs.

a Percentage of tested variants from each class that are eVariants (eV), left) or lead eVariants (right) in the SV/STR-only eQTL. Asterisks indicate significant enrichment or depletion of variants among eVariants relative to STRs (FET two-sided, BH alpha < 0.05). b Left panel is a balloon plot where color indicates number of eVariants and size indicates fraction of eVariants in each bin. Right panel shows average number of eGenes per eVariant with 95% confidence intervals. Red points indicate significantly higher numbers of eGenes per eVariant (Mann–Whitney U one-sided, Bonferonni p < 0.05) compared to STRs. c Distribution of the distance of eQTL (left) and lead eQTL (right) variants to the boundary of their eGenes. Percentages indicate the proportion of eQTLs that were at least 250 kb distal to eGene, red asterisks indicate that eQTLs tended to be localized farther from eGenes as compared to STRs (Mann–Whitney U Test one-sided, Bonferonni p < 0.05). Distributions for lead SNV and indel eQTLs were not examined for significant differences relative to STRs. d Fraction of lead eQTLs that were intergenic or overlapped exons, promoters, or introns of their associated eGene or other genes. e Enrichment of lead eQTLs for each class that overlap each genic element compared to variants from all other classes (FET two-sided, BH alpha < 0.05). f Distribution of effect sizes for lead eQTLs that overlapped or did not overlap an exon of their eGene. (G,H) Distribution of absolute effect sizes for SV classes, STRs, and SNV/indels for exonic (g) and non-exonic (h) eQTLs. Vertical dashed lines indicate means. P values are derived from comparing the effect size distributions for mCNVs to the distributions for STRs, SVs, SNVs, and indels (Mann–Whitney U test one-sided, Bonferonni p < 0.05). All p values and odds ratios for (a) and (e) are in Supplementary Figs. S5 and S6. eQTL statistics for SNV and indels are from the joint analysis for all panels.