Hello, Susan,
If you type in your rs number, rs598126, then go to the following
coordinates: chr17:40,703,984-40,716,770 in hg19 and turn on the
UCSC Genes and snp132 tracks, you will will see that your SNP is
in the gene next to HSD17B1 (COASY, as Pauline points out). As a
proximity marker, then, the SNP is a decent indicator of HSD17B1
for the purposes of linkage, etc.
regards,
--b0b kuhn
ucsc genome bioinformatics group
On 7/20/2011 5:49 PM, Pauline Fujita wrote:
> Hello Susan,
>
> Thank you for contacting the UCSC Genome Browser public Mailing list.
>
> To determine the gene(s) with which your SNP coincides, you can go to
> the browser and turn on: the OMIM genes track, the OMIM AV SNPs track
> (which shows allelic variants annotated by OMIM that also have rs
> identifiers from dbSNP), the All SNPs(132) track and one of the gene
> prediction tracks (i.e. UCSC genes). Once you have these tracks turned
> on, search for rs598126 in the position/search box - this will take you
> to the region where your SNP is located and you can see which genes
> overlap with your SNP.
>
> Your SNP looks like it might fall within the COASY gene according to dbSNP.
>
> dbSNP's page for your SNP:
> http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs598126
>
> OMIM's page for the HSD17B1 gene:
> http://omim.org/entry/109684
>
> OMIM's page for the COASY gene:
> http://omim.org/entry/609855
>
> OMIM doesn't have rs598126 annotated for either gene, but their SNP
> annotations are sparse, especially compared to dbSNP.
>
> Best regards,
>
> Pauline Fujita
> UCSC Genome Bioinformatics Group
> http://genome.ucsc.edu
>
>
> On 07/20/11 10:47, Susan Gurney wrote:
>> Hello Ada, Joanna and Francois,
>>
>> Thank you for your new release of the three separate OMIM tracks,
>>
>> However I am an idiot. I need to find out if in fact rs598126 is on gene
>> HSD17B1 for my
>>
>> advisor ASAP as she would like to get the work (long overdue) finally
>> published, so we
>>
>> need to confirm.
>>
>> I can't navigate your site - can you either verity the SNP is on HSD17B1
>> OR tell me
>>
>> how to do so myself?
>> MANY THANKS..!!
>> Susan Gurney
>>
>>
>>
>> _______________________________________________
>> Genome maillist - [email protected]
>> https://lists.soe.ucsc.edu/mailman/listinfo/genome
>
> _______________________________________________
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> https://lists.soe.ucsc.edu/mailman/listinfo/genome
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