[ensembl-dev] GWAS-catalog result missing

[Laurent Gil]

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 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
>
> 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
>
> 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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