Fig. 6
A GWAS regional association plot for type 2 diabetes (T2D) [69] highlighting the perturbed region with the gray line near GIGYF1. B On the left, violin plots showing the normalized expression values of GIGYF1 in cells expressing GIGYF1 enhancer targeting (TGT) gRNAs (red) versus non-targeting (NT) controls (gray). The number of cells in each group is indicated at the top of the violins. On the right, barplot indicating the proportion of cells with TGT or NT gRNAs where expression of GIGYF1 is detected (counts > 0). The number of cells in each group is indicated at the top, and an * indicates the perturbation was significant at the gRNA level. The target-level corrected p-value (FDR) of expression change and a summary log2 fold-change are indicated at the top. C eQTL regional association plot for GIGYF1 expression in naïve CD4+ T cells [33, 70], highlighting the perturbed region in a gray line. D Colocalization plot of the T2D GWAS signal (A) and GIGYF1 eQTL in naïve CD4+ T cells (C), showing that these signals have a 99% posterior probability of being shared. T2D risk colocalizes with decreased GIGYF1 transcript expression. E GWAS regional association plot for rheumatoid arthritis (RA) [71] highlighting the perturbed region in gray near PHF19 and TRAF1. F Same as B but for expression of TRAF1 in cells expressing PHF19 enhancer targeting (TGT) gRNAs (red) versus NT controls (gray). G eQTL regional association plot for TRAF1 expression in naïve CD4+ T cells, highlighting the perturbed region with a gray line [24, 72]. H Colocalization of the RA GWAS signal (E) and TRAF1 eQTL in naïve CD4+ T cells (G), showing that these signals have an 87% posterior probability of being shared. RA risk colocalizes with increased TRAF1 transcript expression. I GWAS regional association plot for allergic and chronic rhinitis [73] highlighting the perturbed area with a gray line near CXCR5. J Violin plots showing the normalized expression values of CD3D in cells expressing targeting (TGT) gRNAs for CXCR5 intergenic element (red) versus NT controls (gray). The number of cells in each group is indicated at the top, and an * indicates the perturbation was significant at the gRNA level. The target-level corrected p-value (FDR) of expression change and a summary log2 fold change are indicated at the top