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Question: How to map SNP rsids to genes and flanks
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gravatar for robjohn70000
2.1 years ago by
robjohn70000 • 130
Nigeria
robjohn70000 • 130 wrote:

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
genome snp sequence R gene • 792 views
ADD COMMENT • link •
modified 2.1 years ago by Emily_Ensembl ♦ 21k • written 2.1 years ago by robjohn70000 • 130

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

ADD REPLY • link written 2.1 years ago by Pierre Lindenbaum ♦ 134k

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 written 2.1 years ago by zx8754 ♦ 10.0k
2
gravatar for Emily_Ensembl
2.1 years ago by
Emily_Ensembl ♦ 21k
EMBL-EBI
Emily_Ensembl ♦ 21k wrote:

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.
ADD COMMENT • link modified 2.1 years ago • written 2.1 years ago by Emily_Ensembl ♦ 21k
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