[ensembl-dev] Difference in location data for a dbsnp id.

Rohan M rohan7799 at gmail.com
Thu Jan 30 07:09:45 GMT 2014


Hi Sarah, Will,

  Thanks a lot for the reply. It was the version issue.  I updated the
source code to  API - 74 and got back the correct results.

Thanks again.
Regards,



On Wed, Jan 29, 2014 at 5:14 PM, Will McLaren <wm2 at ebi.ac.uk> wrote:

> Hi Ron,
>
> The mapping provided by dbSNP changed between builds (137 in e!72 and 138
> in e!74).
>
> Here you can see the old position on the e!72 archive:
>
> http://e72.ensembl.org/Homo_sapiens/Variation/Summary?v=rs3064744
>
> Regards
>
> Will McLaren
> Ensembl Variation
>
>
> On 29 January 2014 11:29, Rohan M <rohan7799 at gmail.com> wrote:
>
>> Hi All,
>>
>>   I'm using the code snippet given at by ensemble api tutorial, under the
>> section - "Variations, Flanking sequences and Genes"
>> http://asia.ensembl.org/info/docs/api/variation/variation_tutorial.html
>>  I added api version line to the original code and I'm running the script
>> for dbsnp ID 'rs3064744'
>>
>> Here is the output -
>>
>> The API version used is 72
>>
>> rs3064744,-/TA,NMD_transcript_variant,5_prime_UTR_variant,intron_variant,downstream_gene_variant,upstream_gene_variant,feature_elongation,regulatory_region_variant,TATATATATA[-/TA]AGTAGGAGAG,2:234668895-234668894,,ENSG00000242515,,ENSG00000244474,,ENSG00000167165,,ENSG00000243135,,ENSG00000167165,,ENSG00000178836,,ENSG00000167165,,ENSG00000178836,,ENSG00000167165,,ENSG00000244122,,ENSG00000244474,,ENSG00000241635,,ENSG00000240224,,ENSG00000167165,,ENSG00000178836,,ENSG00000241635,,ENSG00000242366,,ENSG00000242515,,ENSG00000178836,,ENSG00000241119,,ENSG00000167165
>>
>>
>> Why does the location retrieved ( 2:234668895-234668894 ) is not matching
>> with the one present on the web?
>> On the web interface it says - Chromosome *2*: between *234668880* and
>> *234668881*
>>
>>
>> http://asia.ensembl.org/Homo_sapiens/Variation/Summary?r=2:234668381-234669380;v=rs3064744;vdb=variation;vf=2706024
>>
>> Could somebody explain what is wrong?
>>
>> Thanks,
>>
>> --
>> Ron
>>
>>
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