How to map SNP rsids to genes and flanks
Hi,
I have a long list of human genes like this:
ATR, BAK1, BAX ......
I will like to extract all snps in this region: 1KB of sequence (5') + gene + 1kb of sequence (3'). How can I easily carry out this extraction? Thanks
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Emily
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robjohn70000
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robjohn70000
1 answer
Use Ensembl BioMart. Use the gene database, filter by the gene names and get the variants as attributes. Here's a help video to get you started with BioMart.
Alternatively, Ensembl REST API. Use the lookup endpoint to get the Ensembl IDs, then use the overlap endpoint to get the variants overlapping the region. Use your favourite programming language to link the endpoints together, you can get help doing this using this online course.
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see How To Map A Snp To A Gene Around +/- 60Kb ? but replace the WHERE clause with the proteinID.
Search for "map SNP to genes", there has been asked many times before, see links at: C: Assigning SNPs to gene names based on genomic coordinates