LocusZoom: regional visualization of genome-wide association scan results.

Bioinformatics
Randall J PruimCristen J Willer

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. 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.

References

Jun 5, 2002·Genome Research·W James KentDavid Haussler
May 6, 2008·Nature Genetics·Ruth J F LoosKaren L Mohlke
Nov 1, 2008·Bioinformatics·Andrew D JohnsonPaul I W de Bakker
Dec 9, 2008·Nature Genetics·Sekar KathiresanL Adrienne Cupples
Feb 7, 2009·Genetic Epidemiology·Eric JorgensonJohn S Witte
Oct 9, 2009·Nature·Teri A ManolioPeter M Visscher
Feb 5, 2010·Bioinformatics·William S BushMarylyn D Ritchie
Feb 23, 2010·Bioinformatics·Armin O SchmittGudrun A Brockmann

❮ Previous
Next ❯

Citations

Feb 23, 2011·Human Genetics·Guillaume Lettre
May 15, 2013·Human Genetics·David B KantorJoel N Hirschhorn
Mar 12, 2013·Journal of Bone and Mineral Metabolism·Andrew MayZané Lombard
Aug 27, 2013·Journal of the Association for Research in Otolaryngology : JARO·E Kaitlynn AllenMichèle M Sale
Jun 20, 2012·Brain Imaging and Behavior·Shubhabrata MukherjeeUNKNOWN Alzheimer’s Disease Neuroimaging Initiative
Mar 14, 2014·The Lancet. Respiratory Medicine·Michael H ChoUNKNOWN NETT Genetics, ICGN, ECLIPSE and COPDGene Investigators
Aug 4, 2012·Twin Research and Human Genetics : the Official Journal of the International Society for Twin Studies·Nic M NovakArthur W Toga
Aug 30, 2012·European Journal of Human Genetics : EJHG·Jie HuangYun Li
Apr 18, 2013·European Journal of Human Genetics : EJHG·Robert W DaviesRuth McPherson
Apr 17, 2012·Nature Genetics·Jason L SteinUNKNOWN Enhancing Neuro Imaging Genetics through Meta-Analysis Consortium
Sep 4, 2012·Nature Genetics·Elizabeth G HollidayUNKNOWN Wellcome Trust Case Control Consortium 2
Mar 5, 2013·Nature Genetics·Mark M IlesUNKNOWN Q-MEGA and AMFS Investigators
Mar 5, 2013·Nature Genetics·Lars G FritscheUNKNOWN AMD Gene Consortium
Apr 16, 2013·Nature Genetics·Tasha E FingerlinDavid A Schwartz
Jun 12, 2013·Nature Genetics·UNKNOWN International Genetics of Ankylosing Spondylitis Consortium (IGAS)Matthew A Brown
May 31, 2011·Nature Genetics·Omar M E AlbaghaUNKNOWN Genetic Determinants of Paget's Disease (GDPD) Consortium
Jun 28, 2011·Nature Genetics·Tuomas O KilpeläinenRuth J F Loos
Oct 11, 2011·Nature Genetics·Stuart MacgregorNicholas K Hayward
Oct 11, 2011·Nature Genetics·Jennifer H BarrettUNKNOWN GenoMEL Consortium

❮ Previous
Next ❯

Software Mentioned

Python
LocusZoom
SQLite
LocusZoom Python application
SNAP
R

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.