Fig. 3

Functional regulatory elements and PPI enrichment analysis. a Heat map showing DNase 1 hypersensitive sites (DHSs) and histone marks enrichment analysis of the set of pleiotropic variants. GenomeRunner web server was used to determine whether the set of pleiotropic SNPs significantly co-localize with regulatory genome annotation data in 127 cell types from the Roadmap Epigenomics project. First column shows cell types grouped and colored by tissue type (color-coded as indicated in the legend). Tissues relevant for the autoimmune diseases studied as well as other tissues for which any of the analyzed functional annotations showed a significant enrichment p value (p < 0.05 after FDR correction) are shown. The remaining four columns denote the analyzed functional annotations, DHSs, H3K27ac, H3K4me1, and H3K4me3. Results of the enrichment analysis are represented in a scale-based color gradient depending on the p value. Blue indicates enrichment and white indicates no statistical significance after FDR adjustment. b Interaction network formed for the set of common genes. Direct and indirect interactions among genes shared by different disease subgroups were assessed using STRING. Plot shows results of the “molecular action” view such that each line shape indicates the predicted mode of action (see legend). Genes involved in the biological pathways enriched among the set of pleiotropic loci (Additional file 2: Table S10) are shown in color: red: Th1 and Th2 cell differentiation; green: Th17 cell differentiation; yellow: Jak-STAT signaling pathway; blue: T cell receptor signaling pathway