Hi Hadas, You can download text dumps of any database table by going to the "Annotation database" links on the downloads page: http://hgdownload.cse.ucsc.edu/downloads.html. The chrom name, position and function are in the snp132 table. There is another (much smaller) table, snp132CodingDbSnp, that contains annotations of the effects of SNPs on translated protein sequence.
For the hg18 assembly, the latest build from dbSNP is 130, so look for the snp130 and snp130CodingDbSnp tables. Note that the tables are quite large; I recommend downloading them via one of the methods outlined on the downloads page instead of via http. To see a description of the fields in the tables and to read more about the SNP tracks at UCSC, go to the main Genome Browser page (http://genome.ucsc.edu/cgi-bin/hgTracks), scroll to the "Variation and Repeats" section, and click on the blue track names, "All SNPs(132)" and "SNPs (130)." There is a "view table schema" link on that page. If you have further questions, please feel free to contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 08/28/11 02:26, Hadas Ner Gaon wrote: > Dear UCSC team > how can i down load the whole dbSNP from assembly 18 and 19. i need > the chr name, position, and if it possible also the gene and the function of the SNPs > Regards, > Hadas Ner-Gaon > > Hadas Ner-Gaon , Ph.D. > The Rubin lab > The Shraga Segal Dept. of Microbiology and Immunology & NIBN > Ben Gurion University > > Building 39, room -113 > POB 653, Beer Sheva 84105, Israel > Phone: 08-6477180 > email: [email protected] > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
