Super-enhancers are a large cluster of transcriptionally active enhancers enriched in enhancer-associated chromatin characteristics. Compared to typical enhancers, super-enhancers are larger, exhibit higher transcription factor density, and are frequently associated with key lineage-specific genes that control cell state and differentiation in somatic cells.

Here, we developed a comprehensive super-enhancer database of human, mouse, Arabidopsis and maize (SEdb 3.0, http://www.licpathway.net/sedb), which aims to provide a large number of available resources on human, mouse, Arabidopsis and maize super-enhancers. The potential functions of super-enhancers in the regulatory network are also annotated in the database. The current version of SEdb 3.0 has recorded a total of 3,481,072 SEs from 5,387 samples, including 3,389 human samples, 1,962 mouse samples, 21 Arabidopsis samples and 15 maize samples. Furthermore, SEdb 3.0 also provides detailed genetic and epigenetic annotation information on super-enhancers. The information includes common SNPs, motif changes, expression quantitative trait loci (eQTL), risk SNPs, transcription factor binding sites (TFBSs), CRISPR/Cas9 targets, DNase I hypersensitive sites (DHSs), chromatin accessibility regions, methylation sites, chromatin interaction regions, TADs and eRNAs. For the in-depth analysis of super-enhancers, SEdb 3.0 will help clarify the functions related to super-enhancers and discover potential biological effects.