PolyPhen

Predicts if a non-synonymous SNP alters an amino acid in a protein resulting in structural changes (damaged or benign) in a protein.

ESEFinder

Predicts if a coding SNP is located in a exonic splicing enhancer motif, which would diminish the motif with a different allele.

Rescue-ESE

Predicts if a coding SNP is located in a exonic splicing enhancer motif, which would diminish the motif with a different allele.

FAS-ESS

Predicts exonic splicing silencer for each SNP allele

TFSearch

Predicts if a non-coding SNP alters the transcription factor binding site of a gene

PolyMAPr

Programs for polymorphism database mining, annotation, and functional analysis

PupaSNP

A web tool for finding SNPs with putative effect at transcriptional level

SNPSeek

A web based interface to human SNPs, frequencies, and annotation data

SNPselector

A web tool for selecting SNPs for genetic association studies