[ensembl-dev] associated or reported gene for phenotypes

[William Spooner]

Hi Mark,

Ensembl only explicitly associates a gene with a variant when it is
within 5kb upstream/downstream. Your SNP is outside this range. You
can query for SNPs that are outside this range by calculating the
location and using BioMart or the Ensembl Perl API. Direct SQL is not
guaranteed to work.

Best,

Will

On Thu, Apr 21, 2016 at 8:36 PM, Mark Miller <Mark.Miller at instem.com> wrote:
> How can I programmatically retrieve variants that are associated with a
> phenotype and ASSOCIATED with a gene, even if the variant is not strictly
> within a gene’s boundaries?
>
>
>
> If you visit
> http://useast.ensembl.org/Homo_sapiens/Gene/Phenotype?db=core;g=ENSG00000073756;r=1:186671791-186680427#ALL_tablePanel,
> under “ALL associated variants” you will see rs10489403 associated with
> hematocrit phenotypes.
>
>
>
> If I query biomart for variants and phenotypes associated with
> ENSG00000073756, rs10489403 is not listed.
>
>         <Dataset name = "hsapiens_snp" interface = "default" >
>
>                <Filter name = "ensembl_gene" value = "ENSG00000073756"/>
>
>                <Attribute name = "refsnp_id" />
>
>                <Attribute name = "ensembl_gene_stable_id" />
>
>                <Attribute name = "associated_gene" />
>
>         </Dataset>
>
>
>
> If I look for rs10489403 in the web interface or biomart, I see that it is
> intergenic between PGTS2 and PLA2G4A.
>
>         <Dataset name = "hsapiens_snp" interface = "default" >
>
>                <Filter name = "snp_filter" value = "rs10489403"/>
>
>                <Attribute name = "refsnp_id" />
>
>                <Attribute name = "ensembl_gene_stable_id" />
>
>                <Attribute name = "associated_gene" />
>
>         </Dataset>
>
>
>
> It doesn’t seem like associated_gene  is a filterable field.  How can I
> query biomart, or MySQL directly,  with ENSG00000073756 as my gene of
> interest and retrieve rs10489403 as a variant which has PTGS2/
> ENSG00000073756 as an associated gene?
>
>
>
> Thanks,
>
> Mark
>
>
>
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-- 
William Spooner
Chief Science Officer
M: +44 (0)7779663045 | T: @wspoonr | L: linkedin
Eagle Genomics Ltd | http://www.eaglegenomics.com
eaglediscover: Winner of Bio-IT World 2016 Best of Show, knowledge management