Hi Carla, Sometimes dbSNP has new data that we have yet to download (they continually update their data; we only update it when a new build is available).
However, in the case of rs78369038, the SNP is present in the "All SNPs(135)" track, but not in the "Common SNPs(135)" track, which is the one that is displayed by default in the hg19 browser. If you put "rs78369038" in the position/search box, you will see a list of tracks in which it appears, and when you click on the link, the track will automatically open. Starting with build 135, there are 4 separate SNP tracks, described on the SNP track description pages: Common SNPs(135) - SNPs with >= 1% minor allele frequency (MAF), mapping only once to reference assembly. Flagged SNPs(135) - SNPs < 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as "clinically associated" -- not necessarily a risk allele! Mult. SNPs(135) - SNPs mapping in more than one place on reference assembly. All SNPs(135) - all SNPs from dbSNP mapping to reference assembly. I hope this information is helpful. If you have further questions, please contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 5/9/12 11:49 AM, Gallagher, Carla wrote: > Hello, > Can you please tell me why an rs number would appear on NCBI, but is not present in the UCSC genome browser? The particular snp I am referring to is rs78369038 . > > Thanks, > Carla > > -- > Carla J. Gallagher, PhD > Assistant Professor > Public Health Sciences and Pharmacology > Penn State College of Medicine > 500 University Drive CH69 > Hershey, PA 17033 > Phone: 717-531-2973 > Fax: 717-531-0480 > [email protected]<mailto:[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
