[ensembl-dev] list of SNPs with a phenotype, sql help

Nathalie Conte nconte at ebi.ac.uk
Thu Oct 9 11:27:11 BST 2014

I am trying to build a sql query in order to select all SNPs (germline and somatic, ie rs1223) associated with a phenotype.(ie diabetes) using sql command.
I started building a sql query connecting different tables in homo_sapiens_variation_77_38 database in order to connect the variation table (variation_id, rs1223)and the phenotype table where the description of the phenotype is (ie diabetes).
Looking at the schema http://www.ensembl.org/info/docs/api/variation/variation-database-schema.pdf , I am linking variation table through variation, variation_attrib, phenotype_feature_attrib, feanotype_feature, and phenotype.
It seems that variation_attri table is empty, so I cannot link the data
mysql -hensembldb.ensembl.org -uanonymous -e"SELECT * FROM  variation_attrib   LIMIT 10;" homo_sapiens_variation_77_38 command will return no  result.
Could you please help me forward suggestion another path to link variation.variation_id to phenotype.description, or suggest directly a sql command?
Thanks in advance

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