Question

How to map SNP rsids to genes and flanks

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5.9 years ago

robjohn70000 ▴ 160

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

SNP gene R sequence genome • 2.5k views

ADD COMMENT • link updated 5.9 years ago by Emily 24k • written 5.9 years ago by robjohn70000 ▴ 160

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see How To Map A Snp To A Gene Around +/- 60Kb ? but replace the WHERE clause with the proteinID.

ADD REPLY • link 5.9 years ago by Pierre Lindenbaum 164k

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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

ADD REPLY • link 5.9 years ago by zx8754 12k

score 2 · Answer 1 · 2019-01-16

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.