Fig. 4

Encyclopedia and conservation-associated activity score. a Conservation-associated activity plot of a promoter and surrounding region. Color indicates annotation label at a given position. In conservation-associated activity plots, labels are vertically scaled by their conservation-associated activity score, so that the overall height corresponds to a position’s total conservation-associated activity score. The vertical axis indicates the conservation-associated activity score at a given position, colored proportionally to the fraction of the score that derives from each label type. Black boundary bars indicate encyclopedia segments. Black phyloP area indicates the 75th percentile of phyloP scores within 100 bp of a given genomic position. Box-and-arrow pictograms indicate genes, where boxes indicate exons and arrows indicate the direction of transcription. Genome coordinates are relative to genome assembly GRCh37. b Conservation-associated activity plots for additional loci (top to bottom): gene with upstream enhancers; gene with distant enhancer; distal enhancer; regulatory element that is repressed in many cell types; large regulatory domain. In the bottom-left cell type-specific annotation plot, cell types are clustered on the vertical axis. c Distribution of lengths of encyclopedia segments. d Enrichment of conservation-associated activity score at GWAS SNPs from the GWAS Catalog. We ordered genomic positions by their conservation-associated activity score. The solid line indicates the number of GWAS SNPs that fall in the top fraction X of this list. The dashed line indicates the average performance when this ordering is performed using a single annotation (standard deviation over annotations indicated by gray area). The dotted line indicates random performance