[ensembl-dev] GWAS-catalog result missing

[andrew126 at mac.com]

Hi Laurent,

Thanks for the quick response and fix .. smile.

Best,

Andrew


> On Jan 5, 2017, at 6:42 AM, Laurent Gil <lgil at ebi.ac.uk> wrote:
> 
> Dear Andrew,
> 
> This is due to an issue with our import script which missed this NHGRI-EBI GWAS catalog result.
> Thank you for spotting it!
> 
> We just fixed the script and the NHGRI-EBI GWAS catalog data for the variant rs1019670 will be in the next Ensembl release (version 88, planned in March), under the newest dbSNP ID "rs7232 ".
> 
> Best regards,
> Laurent
> Ensembl Variation
> On 04/01/2017 21:27, andrew126 at mac.com <mailto:andrew126 at mac.com> wrote:
>> Hi,
>> 
>> I am using Ensembl API v86, but this appears to be a more general question.
>> 
>> The NHGRI GWAS catalog lists a result for rs1019670 (a result which was added to their catalog 2014-03-14):
>> 
>> https://www.ebi.ac.uk/gwas/search?query=rs1019670 <https://www.ebi.ac.uk/gwas/search?query=rs1019670>
>> 
>> However, neither this result nor the variant is found at ensembl.org <http://ensembl.org/>.  A search of ensembl.org <http://ensembl.org/> for rs1019670 returns rs7232:
>> 
>> http://useast.ensembl.org/Homo_sapiens/Variation/Explore?r=11:60172626-60173626;v=rs7232;vdb=variation;vf=6894 <http://useast.ensembl.org/Homo_sapiens/Variation/Explore?r=11:60172626-60173626;v=rs7232;vdb=variation;vf=6894>
>> 
>> rs1019670 is listed as an “archive dbDNP” entry for rs7232; however, no phenotype data appear curated for rs7232 at ensembl.org <http://ensembl.org/>.
>> 
>> Does the superceding of rs1019670 by rs7232 explain why the GWAS-catalog result is not found in Ensembl?  Is there any way that such results could be mapped instead of left out?
>> 
>> Thanks for any information.
>> 
>> Best regards,
>> 
>> Andrew
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
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