Below is a list of representative tools/models/portals:


Attention-based Transformer model to predict epigenetic information such as chromatin accessibility

To further understand how risk variants contribute to the function of regulatory elements, we used deep learning (DL) models to predict chromatin accessibility from DNA sequences. 

Cis-element Atlas

A web portal for single-cell epigenetic datasets

You can explore cell clusters and annotations identified from single-cell ATAC-seq, as well as genomic tracks. We also offer the downloading of candidate enhancer linked to putative target genes at cell-type resolution

Genetic Variants Allelic TF Binding Database (GVATdb)

A web server for searching SNPs with differential Transcription factors (TF) binding

This database characterizes the allelic binding of 95,886 common human single nucleotide polymorphisms (SNPs, MAF>1% in Eeuropean and Asian populations) to 270 distinct transcription factors (TFs). The SNPs were chosen from neighboring regions (<=500 kb) of 83 risk loci of type 2 diabetes (T2D) that were identified in several genome wide association studies (GWAS). The data were generated using SNP-SELEX


This web-based database provides the RNA binding sites and regulatory elements

Crosslinking immunoprecipitation sequencing (CLIP-seq) technologies have enabled researchers to characterize transcriptome-wide binding sites of RNA-binding protein (RBP) with high resolution. We develop a soft-clustering method, RBPgroup, to various CLIP-seq datasets to group together RBPs that specifically bind the same RNA sites. Such combinatorial clustering of RBPs helps interpret CLIP-seq data and suggests functional RNA regulatory elements.