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    LocusTrack: Integrated visualisation of GWAS results and genomic annotation.

  • Citation: "LocusTrack: Integrated visualization of GWAS results and genomic annotation" G Cuellar-Partida, ME Renteria, S MacGregor - Source Code for Biology and Medicine, 2015
  • Update (28/09/14): Population reference updated to 1000 Genomes 2013-05-02 phase 3 release
  • Summary:LocusTrack is a web-based application that creates visual representations of regional GWAS results and integrates user-specified annotation tracks, along with other features such as linkage disequilibrium (LD) and genes within the region of interest.
  • Main features:
    • Generates GWAS regional plots in a LocusZoom1 or SNAP2 fashion (panel a).
    • Displays the genes within the region along with the orientation of their transcribed strand and their exons/introns (panel b).
    • Integrates annotation tracks from the UCSC genome-browser3 hg19 (Human Genome version 19), linkage desequilibrium of the different 1000 Genomes project populations, as well as user custom annotation tracks (panel c).


  • References
    1. Randall J. Pruim et al. LocusZoom: regional visualization of genome-wide association scan results. Bioinformatics Sep 15, 2010; 26(18): 2336–2337. doi: 10.1093/bioinformatics/btq419. Epub 2010 Jul 15.
    2. Broad Institute. SNP Annotation and Proxy Search. http://www.broadinstitute.org/mpg/snap.
    3. Karolchik D. et al. The UCSC Genome Browser database: 2014 update. Nucleic Acids Research 2014 Jan;42(Database issue):D764-70. doi: 10.1093/nar/gkt1168. Epub 2013 Nov 21.
  • Manage files: In order to generate plots, please upload your GWAS result files through 'Manage files -> Results' and follow the instructions. To add custom annotation tracks, please go to 'Manage files -> Custom tracks' and follow the instructions.
  • Generate plot: Once you have uploaded GWAS results file(s) and desired custom tracks, you can then generate LocusTrack plot by clicking in 'Generate Plot' and by following the instructions.
  • Any questions or enquiries regarding LocusTrack: Gabriel.Cuellar@qimrberghofer.edu.au