scEnhancer: a single-cell enhancer resource with gene annotation across hundreds of tissue/cell types in three species


The database provides single-cell enhancer annotation in three species, including human (hg19), mouse (mm9), and fly (dm3). The consensus enhancers were identified based on single-cell datasets of scATAC-seq. Currently, scEnhancer contains 14,527,776 enhancers and 63,658,600 enhancer-gene interactions for 775 tissue/cell types. The database allows users to search the enhancers/genes in simple and advanced ways. Simple Search: (1) Search the single-cell enhancers within a given genomic region in any tissue/cell types; (2) Compare the single-cell enhancers across different single-cell tissue/cell types; (3) identify the single-cell enhancers associated with a particular gene; (4) Compare the single-cell enhancers of the same gene accross different tissue/cell types; (5) predict the regulatory elements for a list of genomic regions. Advanced Search: (1) Graphically display the differences of different tissue/cell types by enhancer clustering; (2) Identification of tissue/cell type-specific enhancers at the single-cell level.

Simple Search

Search single-cell enhancers by region:

Search single-cell enhancers by gene:


Please select species to show tissue/cell types ※

Threshold to determine the gene-enhancer interactions: 

Tissue/Cell types: 



Compare single-cell enhancers across tissue/cell types:

Compare single-cell enhancers of gene across tissue/cell types:

Predict target genes for genomic regions at single-cell level (e.g. peaks from ChIP-Seq):

Or load peaks from file

Please select species to show all tissue/cell types ※

Advanced Search

Display the differences among tissue/cell types by single-cell enhancer clustering (batch information):

Identification of tissue/cell type-specific enhancers at the single-cell level (batch information):


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