Table 1 Publicly available functional annotation programs
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 | 22955989 | |
FORGE | Web server | rsID | Overlapping DNase1 hotspots for SNP(input) | DNase1 hotspot | ||
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 | 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 | 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 | 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) | 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 | 26272984 |