Using a variety of publicly available bioinformatics tools, we assess the functional effects of SNPs along the following four major categories: protein coding, splicing regulation, transcriptional regulation and post-translation effects. The tools, PolyPhen (as of 15 August 2007) (6), SIFT (as of 15 August 2007) (7), SNPeffect (version 2.0) (8), SNPs3D (as of 15 August 2007) (9) and LS-SNP (as of 15 August 2007) (10) are used to identify non-synonymous deleterious SNPs; ESEfinder (release 3.0) (11), RescueESE (as of 15 August 2007) (12), ESRSearch (as of 15 August 2007) (13) and PESX (as of 15 August 2007) (14) are used to identify SNPs in exonic splice regions; The Ensembl database (release 42) (4) is used to identify nonsense SNPs and SNPs in intronic splice sites; TFSearch (ver. 1.3) (15) and Consite (as of 15 August 2007) (16) are used to identify transcriptional regulatory SNPs in promoter regions; The Ensembl (release 42) (4) and GoldenPath (downloaded 12 December 2006) (17) databases are used to identify SNPs in other transcriptional regulatory regions (e.g. microRNA, cpgIslands); KinasePhos (as of 15 August 2007) (18),
