Hello Christoph, Unfortunately we don't have all the information that you are looking for -- but this download file from dbSNP might help:
ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/database/organism_data/b135_SNPContigLocusId_37_3.bcp.gz That is dbSNP's build 135, with chromosome coordinates in GRCh37 (hg19) -- currently, our snp135 tables are under development and available only on our test server, but most rs IDs from older snp* tables should still appear in NCBI's build 135 files. (If they don't, they have been retracted or merged into another SNP id). Its columns are defined here: http://www.ncbi.nlm.nih.gov/projects/SNP/snp_db_table_description.cgi?t=SNPContigLocusId ... actually, that is slightly outdated: several new columns have been added, see the b135_SNPContigLocusId_37_3 stanza in this file: ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/database/organism_schema/human_9606_table.sql.gz The first column, snp_id, corresponds to our tables' "rs12345" IDs but without the "rs". The file does not include exon numbers, but for variants in coding regions, it does give start and stop in transcript coordinates (mrna_start (19th) and mrna_stop (20th) columns). dbSNP might also be able to help: [email protected] <mailto:[email protected]> Hopefully this information was helpful and answers your question. If you have further questions or require clarification feel free to contact the mailing list at [email protected]. Regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 11/9/11 1:46 PM, Christoph Lossin wrote: > Assembly: hg19 > Track: ??? > Location: chr2:167,051,704-167,232,497 > > Browser: Latest Chrome > OS: Windows 7 > > Please see attached doc and question at very end. > > -- > Christoph Lossin, Ph.D. > UC Davis, School of Medicine - Department of Neurology > 4635 2nd Ave - Research I, Suite 1004A > Sacramento, CA 95817 > Office: (916) 703-5511 > Lab: (916) 703-5510 > Fax: (916) 703-5512 > > +++++++++++++++++++++++++++++++++ > The content of this message is solely intended > for the initial recipient. If you have received this > message in error, please disregard it, delete it, > and do not use or forward any information > associated with this email in any way. > +++++++++++++++++++++++++++++++++ > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
