Question: dbSNP build in ENSEMBL biomaRt?
gravatar for 09meh
20 months ago by
09meh0 wrote:

I'm wondering how to determine what dbSNP build (i.e. 150 or 151) the variation annotations are based on. For example, I can find that for GRCh37, this is based on Ensembl Variation 94. The SNP attributes state that the source is dbSNP but not what build:

grch37 = useMart(biomart="ENSEMBL_MART_ENSEMBL", host="", path="/biomart/martservice")
               biomart               version
1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 94
2     ENSEMBL_MART_SNP  Ensembl Variation 94
3 ENSEMBL_MART_FUNCGEN Ensembl Regulation 94
variation = useMart(biomart="ENSEMBL_MART_SNP", host="", path="/biomart/martservice")
12 hsapiens_snp
12 Human Short Variants (SNPs and indels excluding flagged variants) (GRCh37.p13)
12 GRCh37.p13

snps = useMart(biomart="ENSEMBL_MART_SNP", host="", path="/biomart/martservice",dataset="hsapiens_snp")

getBM(attributes=c('refsnp_id','refsnp_source',"refsnp_source_description" ,'chr_name','chrom_start','chrom_end','minor_allele','minor_allele_freq','minor_allele_count','consequence_allele_string'), filters = 'snp_filter', values ="rs123", mart = snps)

  refsnp_id refsnp_source
    1     rs123         dbSNP
                                     refsnp_source_description chr_name chrom_start
    1 Variants (including SNPs and indels) imported from dbSNP        7    24966446
      chrom_end minor_allele minor_allele_freq minor_allele_count
    1  24966446            C          0.292133               1463
    1                       C/A

1) Is this information available programtically through biomaRt? 2) If not, is the best place to find this information? It unfortunately looks like the documentation link on this page ( is currently broken.

dbsnp biomart ensembl • 871 views
ADD COMMENTlink modified 20 months ago by Emily_Ensembl21k • written 20 months ago by 09meh0

An additional source of confusion: searching for individual SNPs on the GRCh37 ENSEMBL website (i.e.;v=rs123;vdb=variation;vf=119) gives information from dbSNP build 150: "Original source: Variants (including SNPs and indels) imported from dbSNP (release 150)" despite "Ensembl GRCh37 release 94" stated at the bottom of the page. So perhaps we can't assume that is true for all Ensembl 94/GRCh37 data?

ADD REPLYlink modified 20 months ago • written 20 months ago by 09meh0

Tagging: Emily_Ensembl

ADD REPLYlink written 20 months ago by genomax87k
gravatar for Emily_Ensembl
20 months ago by
Emily_Ensembl21k wrote:

GRCh37 is on dbSNP 150. In our release next month it will be updated to 151.

ADD COMMENTlink written 20 months ago by Emily_Ensembl21k
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