Map SNP names to gene symbol

Question

[I am]

I have SNP IDs in this format: rs3094315, rs3115860.

Now, I want to map these snp ids to gene symbols in which this snp is present.

Can some one help me in this?

[Neilfws]

Please search this site for previous answers with keywords "biomart" and "snp".

[zx8754]

Related post: Get gene names from rs SNP ids

Answer 1

[Madhan]

Probably this may answer your question:

How To Map A Snp To A Gene Around +/- 60Kb ?

Else, just have a look at this blog and also comments where they have talked about various methods.

http://www.gettinggeneticsdone.com/2011/06/mapping-snps-to-genes-for-gwas.html

If you SNP ids aren't huge, you can try some web based tools like: http://pfs.nus.edu.sg

Or use the perl modules or downloads from UCSC browser (explained in the blog and also in the biostar link I have provided)

Answer 2

[Chris]

The database dumps from dbSNP have those mappings. Of interest are the organism-specific SNPContigLocusID tables on their ftp server.

The most recent one for human could be found here:

ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/database/organism_data/b135_SNPContigLocusId_37_3.bcp.gz

Answer 3

[Rossella]

If the number of SNPs you need to check is small the easiest way is to use dbSNP (http://www.ncbi.nlm.nih.gov/projects/SNP/). If you need to do it in a script and you have the position of the SNP you can just compare it with tx_start,tx_end info that you can download from UCSC. Just be careful to use the same genome version for both your SNP position and the gene position.

Answer 4

[Raymond301]

PharmGKB has a resource. However it is not a comprehensive list.

http://www.pharmgkb.org/resources/downloads_and_web_services.jsp

Download rsid.zip.