Fig. 4

Mapping the regulatory logic at autoimmune disease risk loci using CMs. a The number of autoimmune disease-associated GWAS loci where a CM was mapped in any of the four immune cell types. b The number of loci where the cmQTL colocalized with a GWAS QTL for least one autoimmune disease (posterior probability (PP) > 0.8 and at least one variant that has a p value of 1e-5 for both GWAS and variant-aCM association). c The number of loci where a CM was mapped categorized per autoimmune disease. d The number of loci with a cmQTL-GWAS colocalization categorized per autoimmune disease. e Summary overview of autoimmune disease risk loci that harbor a CM with the associating cmQTL colocalizing with the GWAS variant for at least one disease. The color legend can be found at the lower left of the panel. Abbreviations are spondylitis (AS), celiac disease (CEL), Crohn’s disease (CD), juvenile dermatomyositis (DM), inflammatory bowel disease (IBD), multiple sclerosis (MS), primary biliary cirrhosis (PBC), psoriasis (PSO), rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), type 1 diabetes (T1D), and ulcerative colitis (UC). f Left: example of colocalization of rheumatoid arthritis (RA) GWAS signal and the cmQTLs at the CD40 locus in monocytes. Right: example of colocalization of systemic lupus erythematosus (SLE) GWAS signal and cmQTLs at the BLK locus in LCLs. g Example depicting the SKAP2 locus in neutrophils, one example individual per genotype. h CM activity, SKAP2 and HOXA1 expression stratified by genotype of the highest-ranked candidate-associated variant rs2960785. i Example depicting the C3 locus in neutrophils, one example individual per genotype. j CM activity, C3 and TNFSF14 expression stratified by genotype of the highest-ranked candidate-associated variant rs339392. k Example depicting the TRIM14 locus in monocytes, one example individual per genotype. l CM activity, TRIM14 and CORO2A expression stratified by genotype of the highest-ranked candidate-associated variant rs7867966. In g, i, and k, the red triangles represent the localizations of histone QTLs. In the boxplots, each dot represents one individual and p values were calculated using a Wilcoxon test. p value indications are non-significant (ns) for p value > 0.05, * for 0.01 < p value ≤ 0.05, ** for 0.001 < p value ≤ 0.01, *** for 0.0001 < p value ≤ 0.001, and **** p value ≤ 0.0001