Find SNP location on exon

[venkat.boffin]

Hi all,

I have few SNP rs id's all are coding in exons, i want find the location of SNPs in which exons they are present with respect to its gene.

Help me out..

[bruce01]

dbSNP will give position of SNP. Then you can find which exon that position relates to in a GTF.

[GenoMax]

You could also try Ensembl BioMart (I assume you are working with human rs ID's) and the Ensembl variation database to extract the information you need.

[vivek_]

http://www.ensembl.org/tools.html

Try Variant Effect Predictor from Ensembl tools. (Not sure if this was what GenoMax was referring to as well).

Its pretty comprehensive and you can also check the mutation frequency in 1000 genomes etc if you are looking for a rare variant.