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Finding variants in transcription factor binding motifs with BioMart

Use BioMart to find all short variants that fall in CTCF ENSPFM0042 motifs that have been linked to a phenotype by the GWAS Catalog. Print the variant ID, phenotype description and motif score change.

Start at ensembl.org/biomart/martview. Choose the ENSEMBL Variation database. Choose the Homo sapiens Short Variants (SNPs and indels excluding flagged variants) dataset.

Click on Filters in the left panel. Under GENERAL VARIANT FILTERS: select Phenotype source: NHGRI-EBI GWAS catalog. Under REGULATORY REGION ASSOCIATED INFORMATION FILTERS: select Filter by Binding matrix stable ID(s): ENSPFM0042.

Click on Attributes in the left panel. Under VARIANT ASSOCIATED INFORMATION: select Phenotype description. Under REGULATORY REGION ASSOCIATED INFORMATION: select Motif Score Change.

Click the Results button on the toolbar. Select View All rows as HTML or export all results to a file.