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. 2010 Sep 15;26(18):2336-7.
doi: 10.1093/bioinformatics/btq419. Epub 2010 Jul 15.

LocusZoom: regional visualization of genome-wide association scan results

Randall J Pruim  1 , Ryan P Welch, Serena Sanna, Tanya M Teslovich, Peter S Chines, Terry P Gliedt, Michael Boehnke, Gonçalo R Abecasis, Cristen J Willer
Affiliations

LocusZoom: regional visualization of genome-wide association scan results

Randall J Pruim et al. Bioinformatics. .

Abstract

Genome-wide association studies (GWAS) have revealed hundreds of loci associated with common human genetic diseases and traits. We have developed a web-based plotting tool that provides fast visual display of GWAS results in a publication-ready format. LocusZoom visually displays regional information such as the strength and extent of the association signal relative to genomic position, local linkage disequilibrium (LD) and recombination patterns and the positions of genes in the region.

Availability: LocusZoom can be accessed from a web interface at http://csg.sph.umich.edu/locuszoom. Users may generate a single plot using a web form, or many plots using batch mode. The software utilizes LD information from HapMap Phase II (CEU, YRI and JPT+CHB) or 1000 Genomes (CEU) and gene information from the UCSC browser, and will accept SNP identifiers in dbSNP or 1000 Genomes format. Single plots are generated in approximately 20 s. Source code and associated databases are available for download and local installation, and full documentation is available online.

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Figures

Fig. 1.
Fig. 1.
An example LocusZoom plot showing the HDL cholesterol-associated region near the MMAB gene (Kathiresan et al., 2009).
See this image and copyright information in PMC

References

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