[ensembl-dev] associated or reported gene for phenotypes

Mark Miller Mark.Miller at instem.com
Thu Apr 21 20:36:37 BST 2016


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<http://useast.ensembl.org/Homo_sapiens/Variation/Phenotype?db=core;g=ENSG00000073756;r=1:186671791-186680427;v=rs10489403> associated with hematocrit phenotypes.

If I query biomart for variants and phenotypes associated with ENSG00000073756, rs10489403<http://useast.ensembl.org/Homo_sapiens/Variation/Phenotype?db=core;g=ENSG00000073756;r=1:186671791-186680427;v=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<http://useast.ensembl.org/Homo_sapiens/Variation/Phenotype?db=core;g=ENSG00000073756;r=1:186671791-186680427;v=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<http://useast.ensembl.org/Homo_sapiens/Variation/Phenotype?db=core;g=ENSG00000073756;r=1:186671791-186680427;v=rs10489403> as a variant which has PTGS2/ ENSG00000073756 as an associated gene?

Thanks,
Mark

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