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

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://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/projects/gap/eqtl/index.cgi

OMICStools

Links to a large number of multi-omics tools

http://omictools.com