Can somebody suggest me tools for insilico analysis of intronic and neargene SNP's effects on gene expression or protein structure just like SIFT, PolyPhen for missense SNPs
As far as I know there is no good way to do this yet. My best advice is to use conservation scores; PhastCons and GERP are the two I'm familiar with. You can also limit your search to SNP's that fall in regulatory features, as defined by Ensembl, but I would start by looking at SNPs that fall in highly conserved regions.
A relevant biostar post
GTEx - You can look in their dataset if your SNP is associated with the expression levels of any gene in various tissues: http://www.gtexportal.org/home/#
CADD - "CADD is a tool for scoring the deleteriousness of single nucleotide variants as well as insertion/deletions variants in the human genome.": http://cadd.gs.washington.edu/
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