From: Identification of cis-regulatory sequence variations in individual genome sequences
Genetic variant data | ||
---|---|---|
 | dbSNP | |
 | 1000 Genomes | |
 | HapMap Project | |
Coding variant characterization | ||
 | SIFT | |
 | Polyphen-2 | |
ChIP-Seq data | ||
 | Gene Expression Omnibus (GEO) | |
 | ENCODE project | |
 | PAZAR | |
Motif discovery | ||
 | Meme-ChIP | |
TFBS profiles | ||
 | JASPAR | |
 | PAZAR | |
TFBS databases | ||
 | PAZAR | |
 | ORegAnno | |
TFBS variant characterization | ||
 | Variant effect predictor | |
 | is-rSNP | |
 | rSNP-MAPPER | |
RNA-Seq splice analysis | ||
 | TopHat | |
 | MapSplice | |
Splice enhancer discrimination | ||
 | SFmap | |
 | ESE Finder | |
Data management and visualization | ||
 | Galaxy (tool kit) | |
 | UCSC Genome Browser | |
 | Ensembl BioMart |