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

[Sarah Hunt]

Hi Ron,

Version 72 of the API will be using the version 72 database which used
dbSNP137. The current site is version 74 and uses dbSNP138. It appears
this variant moved between dbSNP releases.

We would recommend you update to the latest API version to access the
latest data, but to check data extracted from the old database, you
would need to use the e!72 archive site:

http://jun2013.archive.ensembl.org/Homo_sapiens/Variation/Summary?r=2:234668381-234669380;v=rs3064744;vdb=variation;vf=2710243

Best wishes,

Sarah

On Wed, Jan 29, 2014 at 11:29 AM, 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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