4 answers
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)
+1 for completion.
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:
Hi Chris - could you provide a URL to this resource?
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
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.
PharmGKB has a resource. However it is not a comprehensive list.
http://www.pharmgkb.org/resources/downloads_and_web_services.jsp
Download rsid.zip.
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