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Table 1 Examples of online data resources and tools for analysis of putative regulatory variants

From: Approaches for establishing the function of regulatory genetic variants involved in disease

Name Description URL
ENCODE Encyclopedia of DNA Elements Project
FANTOM Functional Annotation of the Mammalian Genome project
International Human Epigenome Consortium International Human Epigenome Consortium Data Portal
Roadmap Epigenomics Project NIH Roadmap Epigenomics Mapping Consortium, including links to data
BLUEPRINT European hematopoietic epigenome project
Variant Annotation Integrator (UCSC) Tool for predicting functional effects of variants on transcripts
Variant Effect Predictor (Ensembl) Integrated tool resolving effects of variant on regulatory regions, genes, transcripts and protein
RegulomeDB Tool for functional annotation of SNVs including known and predicted regulatory elements and eQTLs
SNPnexus Integrated functional annotation of SNVs
JASPAR Transcription factor binding profile database
PROMO Transcription factor binding site analysis
MAPPER2 Identification of transcription factor binding sites in multiple genomes
HaploReg Functional annotation of variants on haplotype blocks such as at GWAS loci
GWAS3D Integrated annotation of variants including chromatin interactions
ORegAnno Regulatory annotation database
ConSite Transcription factor binding site detection using phylogenetic footprinting
HGMD Human Gene Mutation Database, including regulatory mutations
Genevar eQTL database integration, search and visualization
eQTL Browser NCBI hosted browser to interrogate eQTL datasets
OMICStools Links to a large number of multi-omics tools
  1. eQTL, expression quantitative trait locus; GWAS, genome-wide association study; SNV, single-nucleotide variant.