[biomart-users] RS SNP ID to Ensembl Gene ID conversion -- only in overlapping genes?

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[biomart-users] RS SNP ID to Ensembl Gene ID conversion -- only in overlapping genes?

Andy McKenzie
Hi everyone, 

I'm using biomaRt and converting from RefSnp ID to Ensembl Gene IDs. From what I understand, the SNP IDs are mapped to gene symbols that contain that SNP. Is this correct? Just want to make sure that it is not "nearby", but actually "within". Below is my code. Thanks, 

Andy 

####

library(biomaRt)

mart.snp = useMart("snp", "hsapiens_snp") 
ensembl = useMart("ensembl", dataset="hsapiens_gene_ensembl") 
 
results = getBM(attributes = c("refsnp_id", "ensembl_gene_stable_id"), 
  filters  = "snp_filter", values = SNP_vector, mart = mart.snp)

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Re: [biomart-users] RS SNP ID to Ensembl Gene ID conversion -- only in overlapping genes?

Thomas Maurel
Dear Andy,

In Ensembl, the variants are mapped on the Transcript level. We annotate variants that overlap a Transcript but also variants that are Upstream or Downstream of a Transcript. If you are only interested in Variants that overlap a Transcript or gene then you can use the “consequence type” filter (called so_parent_name in biomaRt) in the Ensembl snp mart (more information about consequence type on the Ensembl website: http://www.ensembl.org/info/genome/variation/predicted_data.html) and filter out all the variants that are tagged as “upstream_gene_variant” or downstream_gene_variant”.

If you have more questions regarding the Ensembl Variation data, please feel free to email Ensembl helpdesk: [hidden email].

Hope this helps,
Regards,
Thomas
On 29 Jul 2015, at 17:31, Andy McKenzie <[hidden email]> wrote:

Hi everyone, 

I'm using biomaRt and converting from RefSnp ID to Ensembl Gene IDs. From what I understand, the SNP IDs are mapped to gene symbols that contain that SNP. Is this correct? Just want to make sure that it is not "nearby", but actually "within". Below is my code. Thanks, 

Andy 

####

library(biomaRt)

mart.snp = useMart("snp", "hsapiens_snp") 
ensembl = useMart("ensembl", dataset="hsapiens_gene_ensembl") 
 
results = getBM(attributes = c("refsnp_id", "ensembl_gene_stable_id"), 
  filters  = "snp_filter", values = SNP_vector, mart = mart.snp)


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Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

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Re: [biomart-users] RS SNP ID to Ensembl Gene ID conversion -- only in overlapping genes?

Andy McKenzie
Great, thank you! One more question: how many base pairs away from a transcript is considered upstream or downstream? 

Andy 

On Friday, July 31, 2015 at 8:24:54 AM UTC-4, Thomas Maurel wrote:
Dear Andy,

In Ensembl, the variants are mapped on the Transcript level. We annotate variants that overlap a Transcript but also variants that are Upstream or Downstream of a Transcript. If you are only interested in Variants that overlap a Transcript or gene then you can use the “consequence type” filter (called so_parent_name in biomaRt) in the Ensembl snp mart (more information about consequence type on the Ensembl website: <a href="http://www.ensembl.org/info/genome/variation/predicted_data.html" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.ensembl.org%2Finfo%2Fgenome%2Fvariation%2Fpredicted_data.html\46sa\75D\46sntz\0751\46usg\75AFQjCNETEmPCoN0SzZqK760Jy6gJ9oBeVw&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.ensembl.org%2Finfo%2Fgenome%2Fvariation%2Fpredicted_data.html\46sa\75D\46sntz\0751\46usg\75AFQjCNETEmPCoN0SzZqK760Jy6gJ9oBeVw&#39;;return true;">http://www.ensembl.org/info/genome/variation/predicted_data.html) and filter out all the variants that are tagged as “upstream_gene_variant” or downstream_gene_variant”.

If you have more questions regarding the Ensembl Variation data, please feel free to email Ensembl helpdesk: <a href="javascript:" target="_blank" gdf-obfuscated-mailto="IKyZAYRBHgAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">help...@....

Hope this helps,
Regards,
Thomas
On 29 Jul 2015, at 17:31, Andy McKenzie <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="IKyZAYRBHgAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">amc...@...> wrote:

Hi everyone, 

I'm using biomaRt and converting from RefSnp ID to Ensembl Gene IDs. From what I understand, the SNP IDs are mapped to gene symbols that contain that SNP. Is this correct? Just want to make sure that it is not "nearby", but actually "within". Below is my code. Thanks, 

Andy 

####

library(biomaRt)

mart.snp = useMart("snp", "hsapiens_snp") 
ensembl = useMart("ensembl", dataset="hsapiens_gene_ensembl") 
 
results = getBM(attributes = c("refsnp_id", "ensembl_gene_stable_id"), 
  filters  = "snp_filter", values = SNP_vector, mart = mart.snp)


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Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

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Re: [biomart-users] RS SNP ID to Ensembl Gene ID conversion -- only in overlapping genes?

Thomas Maurel
Dear Andy,

We report anything within 5kb of a transcript. I believe you should also exclude the “intergenic_variant” (http://www.sequenceontology.org/browser/current_svn/term/SO:0001628) consequence type as the BioMart filter will return variants tagged with a given term (consequence type) and his children terms (in this case “upstream_gene_variant” and “downstream_gene_variant”).

Hope this helps,
Regards,
Thomas
On 31 Jul 2015, at 15:42, Andy McKenzie <[hidden email]> wrote:

Great, thank you! One more question: how many base pairs away from a transcript is considered upstream or downstream? 

Andy 

On Friday, July 31, 2015 at 8:24:54 AM UTC-4, Thomas Maurel wrote:
Dear Andy,

In Ensembl, the variants are mapped on the Transcript level. We annotate variants that overlap a Transcript but also variants that are Upstream or Downstream of a Transcript. If you are only interested in Variants that overlap a Transcript or gene then you can use the “consequence type” filter (called so_parent_name in biomaRt) in the Ensembl snp mart (more information about consequence type on the Ensembl website: http://www.ensembl.org/info/genome/variation/predicted_data.html) and filter out all the variants that are tagged as “upstream_gene_variant” or downstream_gene_variant”.

If you have more questions regarding the Ensembl Variation data, please feel free to email Ensembl helpdesk: help...@ensembl.org.

Hope this helps,
Regards,
Thomas
On 29 Jul 2015, at 17:31, Andy McKenzie <amc...@gmail.com> wrote:

Hi everyone, 

I'm using biomaRt and converting from RefSnp ID to Ensembl Gene IDs. From what I understand, the SNP IDs are mapped to gene symbols that contain that SNP. Is this correct? Just want to make sure that it is not "nearby", but actually "within". Below is my code. Thanks, 

Andy 

####

library(biomaRt)

mart.snp = useMart("snp", "hsapiens_snp") 
ensembl = useMart("ensembl", dataset="hsapiens_gene_ensembl") 
 
results = getBM(attributes = c("refsnp_id", "ensembl_gene_stable_id"), 
  filters  = "snp_filter", values = SNP_vector, mart = mart.snp)


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Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom


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Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

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