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

[Will McLaren]

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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