Question: How to get a unique target gene for each SNP from different chromosomes/genes in a list at once?
gravatar for cmcouto.silva
3.5 years ago by
São Paulo, Brazil.
cmcouto.silva30 wrote:

Hello, folks!

I have a huge list with SNPs from different chromosomes/genes (human data set), and I wanna know the target genes for each one of them at once (if possible). It would be important to catch only one gene ID per SNP (top rated).

I have tried using the Ensembl Biomart Tool setting the following parameters:

Data set: Human Short Variants (SNPs and indels excluding flagged variants) (GRCh38.p10)


  • Chromosome/scaffold: Chromosomes that I know to have those SNPs
  • Filter by Variant name (e.g. rs123, CM000001) [Max 500 advised]: SNP list (rs*)


  • Chromosome/scaffold name
  • Variant name
  • Gene stable ID

Nevertheless, I got an even bigger list with repeated SNPs and Ensembl ID's for the target genes when I expected unique and usual gene symbol. For example, I would expect "TP53" for "rs1042522", "LAMB3" for "rs80356682", and so on...

Any help/tip would be greatly appreciated!

snp gene • 1.1k views
ADD COMMENTlink modified 3.5 years ago by Alex Reynolds31k • written 3.5 years ago by cmcouto.silva30

bedtools intersect ?

ADD REPLYlink written 3.5 years ago by cpad011214k
gravatar for Maxime Lamontagne
3.5 years ago by
Maxime Lamontagne2.2k wrote:


ADD COMMENTlink written 3.5 years ago by Maxime Lamontagne2.2k
gravatar for Alex Reynolds
3.5 years ago by
Alex Reynolds31k
Seattle, WA USA
Alex Reynolds31k wrote:

You could use BEDOPS bedmap to map positions from vcf2bed to gene names from gff2bed:

$ bedmap --echo --echo-map-id-uniq <(vcf2bed < snps.vcf) <(gff2bed < genes.gff) > answer.bed

This gives you SNP positions and their metadata, along with a list of overlapping gene IDs.

ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by Alex Reynolds31k
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