Fig. 2
Example eQTpLot for LDL cholesterol and the gene ACTN3. eQTpLot was used to generate a series of plots illustrating the colocalization between eQTLs for the gene ACTN3 and a GWAS signal for the LDL cholesterol trait on chromosome 11 using a PanTissue approach as described in example 1. Panel A shows the locus of interest, containing the ACTN3 gene, with chromosomal space indicated along the horizontal axis. The position of each point on the vertical axis corresponding to the p-value of association for that variant with the LDL trait, while the color scale for each point corresponds to the magnitude of that variant’s p-value for association with ACTN3 expression. The directionality of each triangle corresponds to the GWAS direction of effect, while the size of each triangle corresponds to the NES for the eQTL data. The default genome-wide p-value significance threshold for the GWAS analysis, 5e-8, is depicted with a horizontal red line. Panel B displays the genomic positions of all genes within the LOI. Panel C depicts the enrichment of ACTN3 eQTLs among GWAS-significant variants, while panel D depicts the correlation between PGWAS and PeQTL for ACTN3 and the LDL trait, with the computed Pearson correlation coefficient (r) and p-value (p) displayed on the plot