Fig. 7

GCLiPP and PICS2-identified probable causal SNPs guide dissection of cis-regulatory elements in 3′UTR. A Top 15 PICS2 SNPs within GCLiPP peaks with gene location (x-axis) and ranked by PICS2 probability score (y-axis). Diseases associated with SNPs are marked by color. B GCLiPP track of IKZF1 3′UTR. Arrow heads represent gRNA placement to delete two regions (R1 and R2). Vertical dotted line indicates variant location. C Representative IKZF1 protein expression detected by intracellular flow cytometry in Jurkat cells edited with non-targeting control gRNAs (Ctrl), or paired gRNAs targeting IKZF1 3′UTR R1 (blue) or IKZF1 3′UTR R2 deletion (red). D Normalized IKZF1 gMFI for 3 replicate CRISPR targetings from 2 independent experiments. E GCLiPP track of CD5 3′UTR in Jurkats, similar annotations as B. F CD5 expression in Jurkats cells and G primary human CD4 T cells targeted with non-targeting control gRNAs (Ctrl; gray) or CD5 3′UTR gRNAs to induce deletion (red). Histogram shows representative flow cytometry data (left) and normalized geometric mean fluorescence intensity (gMFI) for F 3 replicate CRISPR targeting in 3 independent experiments for Jurkats and G 5 replicates of individuals or pooled individuals from 2 independent experiments for primary human T cells. H GCLiPP track of STAT6 3′UTR in Jurkats. I pSTAT6 gMFI of Jurkat cells or J primary human CD4 T cells polarized to Th2 cells targeted with non-targeting control (Ctrl), STAT6 coding region dual gRNAs (STAT6 KO) or STAT6 3′UTR paired gRNAs following treatment with IL-4 for 0, 5, 10, 15, or 30 min. Data are shown for I 2–3 replicate CRISPR targetings from 3 independent experiments for Jurkats and J 9 individuals or pooled individuals from 3 independent experiments for primary human CD4 T cells