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Question: How to map SNP rsids to genes and flanks
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gravatar for robjohn70000
7 months ago by
robjohn70000 • 120
Nigeria
robjohn70000 • 120 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 • 260 views
ADD COMMENT • link •
modified 7 months ago by Emily_Ensembl ♦ 18k • written 7 months ago by robjohn70000 • 120

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

ADD REPLY • link written 7 months ago by Pierre Lindenbaum ♦ 122k

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 7 months ago by zx8754 ♦ 7.9k
2
gravatar for Emily_Ensembl
7 months ago by
Emily_Ensembl ♦ 18k
EMBL-EBI
Emily_Ensembl ♦ 18k 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 7 months ago • written 7 months ago by Emily_Ensembl ♦ 18k
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