*4.14. Ontology Analysis*

Gene ontology enrichment analysis for enhancers was carried out using GREAT (v3.0.0) [25] with the GO biological process, mouse phenotype, and disease ontologies. Default parameters were used for region-gene associations, unless otherwise specified, and all analyses show top terms, ranked by FDR. Ontology enrichment for sets of genes was carried out using WebGestalt using over-representation analysis and the biological process database, unless otherwise specified. The reference set for comparison was the protein-coding genome and other settings were left as default. All analyses show top terms, ranked by FDR.
