Fig. 3
Example eQTpLot for LDL cholesterol and the gene BBS1, incorporating LD data. eQTpLot was used to generate a series of plots illustrating the colocalization between eQTLs for the gene BBS1 and a GWAS signal for the LDL cholesterol trait on chromosome 11 as described in example 2, specifically within the tissue “Whole_Blood” and with the inclusion of LD data. Panels A, B, and D are generated identically to Figure panels 1A, 1B, and 1C respectively. Panel C depicts a heatmap of LD information of all BBS1 eQTL variants, displayed in the same chromosomal space as panels A and B for ease of reference. Panel E depicts the correlation between PGWAS and PeQTL for BBS1 and the LDL trait, similar to panel 1D, only here a lead variant, rs3741360, is identified (by default the upper-right-most variant on the P-P plot), with all other variants plotted using a color scale corresponding to their squared coefficient of linkage correlation with this lead variant. For reference, the same lead variant is also labelled in panel A