try the code that i provided and then look more closely at the allatt vector
to see the kinds of information you can obtain from biomaRt calls.  you will
need to install biomaRt in a current version of R, use biocLite.

On Thu, Dec 17, 2009 at 10:25 AM, Peter Ganske <Peter.Ganske@hki-jena.de>wrote:

>  Hello everybody,
> sorry for the question. Right, it was not very well-posed.
> Well: I need information about the SNPs. For example:
>
> I have SNP rs6494144 and i want to get informations about the position, the
> allele and if this SNP occour in genes.
>
> I want to generate a gene list for checking the generated list with an list
> i got from a previous paper. I saw that there is the possibility to work
> with PLINK for generating a SNP list with an gene list as the input. So I
> want to do this vice versa.
> Hope, that my question is clearer now.
> Thanks for the help
>
> Peter
>
>
>
>
>
>
> >>> Vincent Carey <stvjc@channing.harvard.edu> 17.12.2009 15:47 >>>
>
> the question is not very well-posed, but you can do something along
> these lines with biomaRt
>
> mart = useMart("snp")
> ds = useMart("snp", data="hsapiens_snp")
> allatt = listAttributes(ds)[,1]
> allfilt = listFilters(ds)[,1]
> getBM(allatt[c(1:5,9,59,60)], filters="refsnp", values="rs206116", mart=ds)
>
> indeed the question of what 'association' between SNP and gene is of
> concern needs to be made much clearer.  if you are interested in the
> eQTL concept, the GGtools package has relevant tools and example data.
>
>
> On Thu, Dec 17, 2009 at 9:27 AM, James W. MacDonald
> <jmacdon@med.umich.edu> wrote:
> > Hi Peter,
> >
> > Peter Ganske wrote:
> >>
> >> Hello everybody, i got  a list of SNPs. Is there a package to get
> >> informations about the association with genes automatically? I want
> >> to check the SNPs and collect some informations about them. Would be
> >> amazing, if anybody can help me out. Thanks in advance Peter
> >
> > Not that I know of. And certainly not something that you can plug in a
> bunch
> > of rs numbers and automagically get all kinds of info returned.
> >
> > Any response depends on what you mean by 'association with genes'. If you
> > mean something naive like 'is this SNP between the 5' and 3' UTR of some
> > gene, then you could use the org.Xx.eg.db package for your organism along
> > with the IRanges package to find SNPs that are 'in' genes.
> >
> > Anything more sophisticated than that will likely require you to write
> your
> > own functions and/or use software outside the Bioconductor project.
> >
> > Best,
> >
> > Jim
> >
> >
> >>
> >>
> >>
> >>
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> > Biostatistician
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