D716–D720 Nucleic Acids Research, 2007, Vol. 35, Database issue doi:10.1093/nar/gkl953 Published online 6 December 2006 Variation resources at UC Santa Cruz Daryl J. Thomas1,2,*, Heather Trumbower2, Andrew D. Kern2, Brooke L. Rhead 2 , Robert M. Kuhn 2 , David Haussler1,2,3 and W. James Kent1,2 1Department of Biomolecular Engineering, 2Center for Biomolecular Science and Engineering and 3Howard Hughes Medical Institute, University of California at Santa Cruz, Santa Cruz, CA, USA Received August 15, 2006; Revised October 21, 2006; Accepted October 23, 2006 ABSTRACT The variation resources within the University of California Santa Cruz Genome Browser include polymorphism data drawn from public collections and analyses of these data, along with their display in the context of other genomic annotations. Pri- mary data from dbSNP is included for many organi- sms, with added information including genomic alleles and orthologous alleles for closely related organisms. Display filtering and coloring is available by variant type, functional class or other annota- tions. Annotation of potential errors is highlighted and a genomic alignment of the variant’s flanking sequence is displayed. HapMap allele frequencies and linkage disequilibrium (LD) are available for each HapMap population, along with non-human primate alleles. The browsing and analysis tools, downloadable data files and links to documentation and other information can be found at http:// genome.ucsc.edu/. INTRODUCTION The development of high throughput platforms to study genomic variation has provided new datasets that have deep- ened our understanding of genome structure and evolution. The single nucleotide polymorphism (SNP) discovery and genotyping platforms (http://www.affymetrix.com/index. affx; http://www.perlegen.com/; http://www.illumina.com/) allow the cost effective generation of deep, dense datasets of human variation. Although many such datasets are publicly available through individual web sites, the disconnected nature of these resources makes it difﬁcult for many biolo- gists to use. The variation resources section of the Genome Browser collects much of these data in a common format in a single location, provides additional variation annotations and allows examination of the data in a genomic context with additional types of information. The primary resource for small scale variation data is dbSNP [http://www.ncbi.nlm.nih.gov/snp/; (1)] which is a repository that collects data from all public projects. These data are presented in the Genome Browser through a display that simpliﬁes comparison with other genomic annotations. In addition, ﬁltering on this track allows increased focus on speciﬁc subsets of the data, such as non-synonymous mutations or variants in conserved regions. Several of the public efforts—HapMap, Affymetrix, Perlegen and SeattleSNPs—are complete enough to warrant additional focus at UC Santa Cruz. Additional analyses of these data can shed new light on genome evolution and help target functional regions, including the identiﬁcation of disease susceptibility loci. Calculations of linkage disequilib- rium (LD) and Tajima’s D0 have been performed, and orthologous alleles have been identiﬁed for human biallelic SNPs. In addition, external groups have contributed other analyses, such as the recombination rates and hotspots and the structural variants. These are all available for integrated display, analysis and download. RESULTS Data types and data dbSNP. We provide mappings of all variant data from dbSNP to the current assembly of our supported species, including human, chimpanzee, mouse, rat, dog and chicken. When a new assembly is released for a given species, dbSNP (1) maps all of the submitted variant data to the new coordinates and releases their build within a few months. Sometimes there are enough new submissions to warrant the develop- ment and release of a new build for an existing assembly. In either case, we then process the new dbSNP build through our pipeline for public release within weeks. In addition to displaying data extracted from dbSNP, the orthologous states from closely related species (e.g. chimpanzee and macaque for the human genome) are identiﬁed using liftOver (2). Also, comparison with the reference sequence shows the direction of insertion/deletion (indel) events (i.e. was there a deletion of bases in the reference sequence, or were new bases inserted?). The pipeline extracts the most relevant *To whom correspondence should be addressed at: Engineering 2, Suite 501, Mail stop CBSE/ITI, Santa Cruz, CA 95064, USA. Tel: +1 831 459 1544; Fax: +1 831 459 1809; Email: daryl@soe.ucsc.edu 2006 The Author(s). This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.