the VariantAnnotation package is what you want.  Well, assuming these are
human SNPs, that is.
It will also annote preceding and following genes for intergenic SNPs.


On Tue, Mar 6, 2012 at 8:24 PM, Kunbin Qu <KQu@genomichealth.com> wrote:

> Hi,
>
> I have a long list of SNP calls, like chr2.161597652 (millions of them),
> and would like to classify them into the following categories: 1) exon, 2)
> intron, 3) UTR, 4) intergenic. For the first 3 categories, it would be
> great if the gene name could also be identified. Can anybody point me to
> some function or package? Thanks.
>
> -Kunbin
>
>
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-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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