Fig. 6

Identification of miRNAs linking edQTL, eQTL, and GWAS signals. a Histograms of the number of differential RNA editing sites induced by miRNA perturbation. The numbers of sites with a significant decrease in RNA editing level are plotted on the left while the numbers of sites with a significant increase in RNA editing level are plotted on the right. The vertical axis labels indicate the cell line, miRNA, and the type of perturbation (KD, knockdown; OE, overexpression). b Example of differential RNA editing sites induced by miRNA perturbation (miR-138-5p knockdown in ND-MSC cells). Horizontal red line indicates 5% FDR. Two vertical red lines indicate a change in RNA editing level of − 5% and 5%. The red dot represents the RNA editing site at chr19:10462087 in the TYK2 gene. c RNA editing level at chr19:10462087 in the TYK2 gene upon miR-138 knockdown in ND-MSC cells. d Cis-regulated RNA editing at chr19:10462087 is associated with cis-regulated gene expression of the TYK2 gene and immune system related GWAS traits. Box plots show the significant association of rs11085725 with the editing level (Φ) at chr19:10462087 and gene expression level of the TYK2 gene within the whole blood (top). Each dot represents data from a particular individual. An example of a whole blood RNA-seq alignment is shown along with gene annotations (RefSeq), annotated ALU elements, annotated RNA editing sites, edQTL SNPs for chr19:10462087, and GWAS SNPs (middle). LD plot (bottom) shows GWAS SNPs (green) linked with the edQTL SNP (purple) in TYK2. e edQTL and eQTL signals of the TYK2 gene colocalize with GWAS signals for neutrophil percentage of white blood cells and systemic lupus erythematosus. Manhattan plots for RNA editing, gene expression, and two GWAS traits are shown (top). Bar plot shows colocalization posterior probabilities between edQTL, eQTL, and GWAS signals (bottom)