You can get the list of the available GRCh37 marts by running the following command: > listMarts(host='grch37.ensembl.org') biomart version 1 ENSEMBL_MART_ENSEMBL Ensembl Genes 2 ENSEMBL_MART_SNP Ensembl Variation 3 ENSEMBL_MART_FUNCGEN Ensembl Regulation 4 ENSEMBL_MART_VEGA Vega 5 pride PRIDE (EBI UK) The following command will give you the list of datasets available for the GRCh37 snp mart: > grch37_snp = useMart(biomart="ENSEMBL_MART_SNP", host="grch37.ensembl.org") > listDatasets(grch37_snp) dataset description version 1 ecaballus_snp Equus caballus Short Variation (SNPs and indels) (EquCab2) EquCab2 2 hsapiens_snp Homo sapiens Short Variation (SNPs and indels) (GRCh37.p13) GRCh37.p13 3 hsapiens_structvar Homo sapiens Structural Variation (GRCh37.p13) GRCh37.p13 4 oanatinus_snp Ornithorhynchus anatinus Short Variation (SNPs and indels) (OANA5) OANA5 5 tnigroviridis_snp Tetraodon nigroviridis Short Variation (SNPs and indels) (TETRAODON8.0) TETRAODON8.0 6 oaries_snp Ovis Aries Short Variation (SNPs and indels) (Oar_v3.1) Oar_v3.1 7 drerio_snp Danio rerio Short Variation (SNPs and indels) (Zv9) Zv9 8 mdomestica_snp Monodelphis domestica Short Variation (SNPs and indels) (monDom5) monDom5 9 cfamiliaris_structvar Canis familiaris Structural Variation (CanFam3.1) CanFam3.1 10 btaurus_snp Bos taurus Short Variation (SNPs and indels) (UMD3.1) UMD3.1 11 mmulatta_snp Macaca mulatta Short Variation (SNPs and indels) (MMUL_1) MMUL_1 12 nleucogenys_snp Nomascus leucogenys Short Variation (SNPs and indels) (Nleu1.0) Nleu1.0 13 mgallopavo_snp Meleagris gallopavo Short Variation (SNPs and indels) (UMD2) UMD2 14 ecaballus_structvar Equus caballus Structural Variation (EquCab2) EquCab2 15 tguttata_snp Taeniopygia guttata Short Variation (SNPs and indels) (taeGut3.2.4) taeGut3.2.4 16 fcatus_snp Felis catus Short Variation (SNPs and indels) (Felis_catus_6.2) Felis_catus_6.2 17 hsapiens_structvar_som Homo sapiens Somatic Structural Variation (GRCh37.p13) GRCh37.p13 18 dmelanogaster_snp Drosophila melanogaster Short Variation (SNPs and indels) (BDGP5) BDGP5 19 rnorvegicus_snp Rattus norvegicus Short Variation (SNPs and indels) (Rnor_5.0) Rnor_5.0 20 pabelii_snp Pongo abelii Short Variation (SNPs and indels) (PPYG2) PPYG2 21 ggallus_snp Gallus gallus Short Variation (SNPs and indels) (Galgal4) Galgal4 22 scerevisiae_snp Saccharomyces cerevisiae Short Variation (SNPs and indels) (R64-1-1) R64-1-1 23 drerio_structvar Danio rerio Structural Variation (Zv9) Zv9 24 mmulatta_structvar Macaca mulatta Structural Variation (MMUL_1) MMUL_1 25 mmusculus_snp Mus musculus Short Variation (SNPs and indels) (GRCm38.p2) GRCm38.p2 26 mmusculus_structvar Mus musculus Structural Variation (GRCm38.p2) GRCm38.p2 27 btaurus_structvar Bos taurus Structural Variation (UMD3.1) UMD3.1 28 ptroglodytes_snp Pan troglodytes Short Variation (SNPs and indels) (CHIMP2.1.4) CHIMP2.1.4 29 sscrofa_structvar Sus scrofa Structural Variation (Sscrofa10.2) Sscrofa10.2 30 hsapiens_snp_som Homo sapiens Somatic Short Variation (SNPs and indels) (GRCh37.p13) GRCh37.p13 31 cfamiliaris_snp Canis familiaris Short Variation (SNPs and indels) (CanFam3.1) CanFam3.1 32 sscrofa_snp Sus scrofa Short Variation (SNPs and indels) (Sscrofa10.2) Sscrofa10.2 To query human GRCh37 snp mart, you can just use one of the following command: 1) For germline data: grch37_snp = useMart(biomart=“ENSEMBL_MART_SNP", host="grch37.ensembl.org", dataset="hsapiens_snp") 2) For the somatic data: grch37_snp_som = useMart(biomart=“ENSEMBL_MART_SNP", host="grch37.ensembl.org", dataset="hsapiens_snp_som") 3) For the structural variation germline data: grch37_structvar = useMart(biomart=“ENSEMBL_MART_SNP”, host="grch37.ensembl.org", dataset="hsapiens_structvar") 4) For the structural variation somatic data: grch37_structvar_som = useMart(biomart=“ENSEMBL_MART_SNP”, host="grch37.ensembl.org", dataset="hsapiens_structvar_som") Hope this helps, Thomas > On 19 Mar 2015, at 19:26, mrprao [bioc] <noreply@bioconductor.org> wrote: > > Activity on a post you are following on support.bioconductor.org <https: support.bioconductor.org=""/> > User mrprao <https: support.bioconductor.org="" u="" 7486=""/> wrote Question: biomaRt: SNP no access to grch37.ensembl.org <https: support.bioconductor.org="" p="" 65831=""/>: > > > Hi, > > How do I access the SNPs (say rs ids to coordinates) from this GRCH37 archive http://grch37.ensembl.org <http: grch37.ensembl.org=""/> archive. > > useMart(biomart="ENSEMBL_MART_ENSEMBL", host="grch37.ensembl.org", path="/biomart/martservice", dataset="?????") > >snp_mart = useMart(biomart="ENSEMBL_MART_ENSEMBL", host="grch37.ensembl.org", path="/biomart/martservice", dataset="SNP") > Error in useDataset(mart = mart, dataset = dataset, verbose = verbose) : > The given dataset: SNP , is not valid. Correct dataset names can be obtained with the listDatasets function. > Calls: useMart -> useDataset > > > > snp_mart = useMart(biomart="ENSEMBL_MART_ENSEMBL", host="grch37.ensembl.org", path="/biomart/martservice", dataset="hsapiens_snp_ensembl") > Error in useDataset(mart = mart, dataset = dataset, verbose = verbose) : > The given dataset: hsapiens_snp_ensembl , is not valid. Correct dataset names can be obtained with the listDatasets function. > Calls: useMart -> useDataset > > > listDatasets(useMart(biomart="ENSEMBL_MART_ENSEMBL", host="grch37.ensembl.org", path="/biomart/martservice")) > dataset description > > 31 hsapiens_gene_ensembl Homo sapiens genes (GRCh37.p13) > > version > > 31 GRCh37.p13 > > > > > There is no SNP dataset either > > > You may reply via email or visit biomaRt: SNP no access to grch37.ensembl.org > -- 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