Fig. 5

Example RA risk enhancers and their target genes. a A genome browser view showing a 250 kp window around the RA risk loci rs2317230. The RA GWAS hit and SNPs in LD are shown in red and overlap two immune enhancer regions. Yellow and orange are used to highlight enhancer locations and point to their target genes whose active TSSs are highlighted with gray. Histone modification tracks show the fold change between ChIP and control read counts. Active histone modifications have red bars next to their labels while repressive marks have blue. Genes on the positive and negative strands are shown in blue and cyan, respectively. b A genome browser view is shown as in a, but around the RA risk loci rs72717009. c Gene expression (normalized log2-transformed values) is plotted versus the genotype at representative enhancer-localized SNPs for the same genes shown in a and b