Gene targets of multiple enhancer variants are highly cell type-specific and functionally related. (A) Percent of H3K4me1 sites that are associated with a PreSTIGE prediction, for all GM12878 cell type-specific H3K4me1 sites (gray) and GM12878-specific sites that contain a GWAS SNP that is associated with the six immune-related disorders (red) (χ², P-value < 0.0001). (B) Cell type specificity (Shannon entropy Q score) of all enhancers in the 12 cell line comparator set (white), GM12878 cell type-specific enhancers (gray), and enhancers containing disease-associated SNPs (red) (Mann-Whitney-Wilcoxon test, P-value < 5.3 × 10⁻⁶). (C) Cell type specificity (Shannon entropy Q-score) of all genes (white), genes associated with a PreSTIGE prediction in GM12878 (gray), and predicted gene targets of disease-correlated SNPs (purple) (Mann-Whitney-Wilcoxon test, P-value < 5.3 × 10⁻⁶). (D) GREAT results for each of the six diseases. Top five significant results are shown for Pathway Commons, GO biological processes/molecular function, and MSigDB pathways categories for each trait.