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
|