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. 2020 Feb 25;11:1041. doi: 10.1038/s41467-020-14483-x

Fig. 3. i-eQTL target regions have evidence for distinct regulation.

Fig. 3

a Local association plots (−log10 FDR-corrected p values for eQTL association), illustrating sharing of the rs113317084 variant (red point) between the i-eQTL-targeted region, DER32583 (green track), and the ge-eQTL-targeted gene, DNAJC15 (blue track). b Local association plot illustrating no sharing of the rs4696709 variant (red point) between the i-eQTL-targeted region, DER10633 (green track), and the ge-eQTL-targeted gene, ABLIM2 (blue track). The detection of reads spanning DER10633 and an annotated exon within ABLIM2 provides compelling evidence that this region represents a novel exon of the gene. c Heterogeneity (distinct vs. shared) of i-eQTL signals, cross-categorised by the strength of evidence linking their target region to a known gene, suggests that most are distinct and likely represent novel regulatory variants acting in a transcript-specific manner. Heterogeneity was determined using a modified beta-heterogeneity test, accounting for the dependency structure arising from within-individual and within-gene correlations. i-eQTL beta-coefficients were compared with that of the known exon with most evidence of association with the i-eQTL target region. All eQTL signals with an FDR-corrected p value for heterogeneity < 0.05 were considered distinct, whereas those with an FDR-corrected p value > 0.05 were considered shared (similar beta-coefficients). d Heterogeneity (distinct vs. shared) of non-standard eQTL classes (gi-eQTLs, e-eQTLs, ex-ex-eQTLs, and i-eQTLs) suggests that many of these classes are distinctly regulated. Heterogeneity was determined using a modified beta-heterogeneity test comparing beta-coefficients from ge-eQTLs to those derived from non-standard eQTL analyses applied to the same gene. This analysis was performed separately for gi-eQTLs (tagging pre-mRNA), e-eQTLs, and ex-ex-eQTLs (tagging splicing) and all i-eQTLs (tagging unannotated expression). All eQTL signals with an FDR-corrected p value < 0.05 were considered distinct, whereas an FDR-corrected p value > 0.05 was taken as evidence of eQTL sharing. Source data are provided as a Source Data file.