Fig. 7: Interpretation of GWAS loci with molQTL.
From: Egg-laying ChickenGTEx resource deciphers context-specific regulatory effects on fertility traits
A UpSetR plot depicting the number of GWAS loci colocalized with four classes of molecular QTL (eQTL, exQTL, enQTL, and sQTL). The inset UpSetR plot shows, within the set of all eQTL–GWAS colocalizations, the breakdown across three eQTL categories: stage-interaction eQTL (stage-ieQTL), stage-specific eQTL (stage_specific), and other eQTL. B Interpretation of GWAS loci for egg number from ages 210 to 400 days, where the GWAS loci colocalize with the sQTL of PIK3R1 but not with the corresponding eQTL. The purple star indicates the SNP with the highest colocalization posterior probability (PPH.4), rs16762093. The −log10(P-values) for the GWAS and molQTL associations are shown in the plot, reflecting the statistical significance of each variant. The color of each point represents the linkage disequilibrium (r²) value between surrounding SNPs and rs16762093. C An example of stage-specific colocalization between the GWAS locus on chromosome 28 for egg number at 210 days and the eQTL of AMH in the ovary. The AMH eQTL exhibits stage specificity, being detected only in the pre-laying stage. The purple star indicates the SNP with the highest colocalization posterior probability (PPH.4), rs314098017. The color of each point represents the linkage disequilibrium (r²) value between surrounding SNPs and rs314098017. The −log10(P-values) for the GWAS and molQTL associations are shown in the plot, reflecting the statistical significance of each variant. The bottom panel shows the effect sizes of rs314098017 on AMH expression across the three laying stages, with bars representing the standard errors of the effect estimates. Sample sizes are as follows: GWAS (n = 12,952), pre-laying stage (n = 116), peak-laying stage (n = 110), and late-laying stage (n = 115).
