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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 https://www.encodeproject.org
FANTOM Functional Annotation of the Mammalian Genome project http://fantom.gsc.riken.jp/5/
International Human Epigenome Consortium International Human Epigenome Consortium Data Portal http://ihec-epigenomes.org/outcomes/ihec-data-portal/
Roadmap Epigenomics Project NIH Roadmap Epigenomics Mapping Consortium, including links to data http://www.roadmapepigenomics.org
BLUEPRINT European hematopoietic epigenome project http://www.blueprint-epigenome.eu
Variant Annotation Integrator (UCSC) Tool for predicting functional effects of variants on transcripts http://www.noncode.org/cgi-bin/hgVai
Variant Effect Predictor (Ensembl) Integrated tool resolving effects of variant on regulatory regions, genes, transcripts and protein http://www.ensembl.org/info/docs/tools/vep/index.html
RegulomeDB Tool for functional annotation of SNVs including known and predicted regulatory elements and eQTLs http://regulomedb.org
SNPnexus Integrated functional annotation of SNVs http://snp-nexus.org/about.html
JASPAR Transcription factor binding profile database http://jaspar.genereg.net
PROMO Transcription factor binding site analysis http://alggen.lsi.upc.es/cgi-bin/promo_v3/promo/promoinit.cgi?dirDB=TF_8.3
MAPPER2 Identification of transcription factor binding sites in multiple genomes http://genome.ufl.edu/mapper/
HaploReg Functional annotation of variants on haplotype blocks such as at GWAS loci http://www.broadinstitute.org/mammals/haploreg/haploreg.php
GWAS3D Integrated annotation of variants including chromatin interactions http://jjwanglab.org/gwas3d
ORegAnno Regulatory annotation database http://www.oreganno.org/oregano/
ConSite Transcription factor binding site detection using phylogenetic footprinting http://consite.genereg.net
HGMD Human Gene Mutation Database, including regulatory mutations http://www.hgmd.org
Genevar eQTL database integration, search and visualization http://www.sanger.ac.uk/resources/software/genevar/
eQTL Browser NCBI hosted browser to interrogate eQTL datasets http://www.ncbi.nlm.nih.gov/projects/gap/eqtl/index.cgi
OMICStools Links to a large number of multi-omics tools http://omictools.com
  1. eQTL, expression quantitative trait locus; GWAS, genome-wide association study; SNV, single-nucleotide variant.