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Table 1 Publicly available functional annotation programs

From: Making sense of GWAS: using epigenomics and genome engineering to understand the functional relevance of SNPs in non-coding regions of the human genome

Tool Type Minimum input Output Epigenetic annotation file used URL PMID
HaploReg Web server rsID Overlapping annotated features and TF motif disruption information for SNPs (input) and correlated SNPs with r2 >0.8 ChromHMM, DNase-seq, a library of position weight matrices (PWMs) from TRANSFAC, JASPAR, and protein binding array (PBM), and eQTL http://www.broadinstitute.org/mammals/haploreg/haploreg_v3.php 22064851
RegulomeDB Web server rsID Overlapping annotated features for SNPs (input) with scores which depend on the combination of overlapping annotated features and UCSC genome browser showing overlapping features TF binding, Dnase-seq, FAIRE, DNase footprinting, eQTL, dsQTL, ChIP-exo and DNA methylation http://www.regulomedb.org 22955989
FORGE Web server rsID Overlapping DNase1 hotspots for SNP(input) DNase1 hotspot http://browser.1000genomes.org/Homo_sapiens/UserData/Forge  
rSNPBase Web server rsID or gene name Proximal or distal transcriptional regulation, miRNA regulation, RNA binding protein mediated regulation, eQTL results for SNPs (input) and correlated SNPs (r2>0.8) histone modification, TF bindings, CpG islands, RBP, miRNA data http://rsnp.psych.ac.cn/ 24285297
FunciSNP R package GWAS index SNP information (chrom:position, rsID, population)in tab-delimited file, biofeature information in .bed format, user‐defined r 2 value Overlapping annotated features for index SNP(input) and correlated SNPs which r2 values are user‐defined Any biofeature annotation information in .bed format https://github.com/labrazil/Coetzee_Seq_Analysis/tree/master/FunciSNP 22684628
GREGOR A package run using perl code A file containing single column of index SNPs, biofeature information in .bed format, user‐defined r 2 value Prioritized variants based on overlap with selected regulatory regions, enrichment analysis with P‐values showing how index SNPs or correlated SNPs are enriched in annotated feature compared to control SNPs Any biofeature annotation information in .bed format http://csg.sph.umich.edu/GREGOR/index.php/site/index 25886982
Enlight Web server rsID, P value Plots showing LD and overlapping annotated features for SNP (input) chromHMM, histone modification, DNA methylation, TF bindings, eQTL, Hi-C or customized BED file for biofeatures http://enlight.usc.edu/index.html 25262152
GWAS3D Web server rsID, P- value TF motif analysis and overlapping annotated features for SNPs (input) 5C, Hi-C, ChIA-PET, ChromeHMM, H3K27Ac, p300, CTCF, DHS (Option for selecting cell lines relevant to disease) http://jjwanglab.org/gwas3d 23723249
motifbreakR R package SNP information in .bed or .vcf format Comprehensive TF binding sites disruption at SNPs (input) TF motif information from ScerTF, FlyFactorSurvey, hpDI, UniPROBE, JASPAR, ENCODE, Homer, Factorbook, HOCOMOCO https://github.com/Simon-Coetzee/motifBreakR-- 26272984