Fig. 2: Enrichment and colocalization analysis of eQTLs and sQTLs with POAG and IOP associations. | Nature Communications

Fig. 2: Enrichment and colocalization analysis of eQTLs and sQTLs with POAG and IOP associations.

From: Integrating genetic regulation and single-cell expression with GWAS prioritizes causal genes and cell types for glaucoma

Fig. 2

Quantile-quantile (Q-Q) plots of POAG cross-ancestry (a) and IOP (b) GWAS -log10 (P-value) compared to expectation for the best eQTL per eGene sets (eVariants with FDR < 0.05) of the most significantly enriched tissues based on adjusted fold-enrichment (colored points), compared to all variants in the GWAS (black points). Grey line represents the diagonal. QTLEnrich (one-sided test; see Methods) was applied to assess GWAS p-value enrichment among the eQTL sets. Bonferroni correction was applied. c Histogram of percent of GWAS loci with ≥1 colocalizing e/sQTL (colocalization posterior probability (CLPP) > 0.01 from eCAVIAR and/or regional colocalization probability (RCP) > 0.1 from enloc) for POAG cross-ancestry, POAG European (EUR) ancestry subset, and IOP European ancestry GWAS meta-analyses. Numbers above the bars represent the number of loci with at least one colocalizing e/sQTL. Red, dark blue, and light blue bars indicate percentage of loci with at least one colocalizing eGene, sGene, or both, respectively. e/sGene, gene with at least one significant e/sQTL. d Scatter plot comparing unique number of e/sGenes that significantly colocalized per GWAS locus versus unique number of e/sGenes tested per locus. Points are color-coded by number of GWAS loci. The black line represents the diagonal. e Violin plots showing the distribution of the unique number of colocalizing eGenes (red), sGenes (dark blue), or both (light blue) per locus for the three GWAS meta-analyses tested. The number of GWAS loci that colocalized with eGenes, sGenes, or both shown in the violin plot are N = 69, 36, 76, respectively, for POAG cross-ancestry, N = 34, 17, 36, respectively, for POAG EUR, and N = 76, 40, 79, respectively, for IOP (Supplementary Data 16). The center line in the box plots contained within each violin plot shows the median, the box edges depict the interquartile range (IQR), and whiskers mark 1.5x the IQR. The violin plot edges represent the minima and maxima values. f, Stacked histogram showing the number of colocalizing e/sGenes per gene biotype for each GWAS. Protein coding (light blue), lincRNA (brown), antisense (grey), pseudogenes (yellow), and other (dark blue).

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