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LocusZoom specifications

Information


Unique identifier OMICS_04408
Name LocusZoom
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python, R
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Cristen J. Willer

Publication for LocusZoom

LocusZoom citations

 (361)
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Genome wide association study identified ATP6V1H locus influencing cerebrospinal fluid BACE activity

2018
BMC Med Genet
PMCID: 5948839
PMID: 29751835
DOI: 10.1186/s12881-018-0603-z
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[…] henotypes were also performed using PLINK software. Genome-wide associations were visualized by a software program (R, version 3.4.0; The R Foundation). Regional associations were visualized with the LocusZoom web tool (http://locuszoom.org/). […]

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Genome wide association study identifies two loci influencing plasma neurofilament light levels

2018
BMC Med Genomics
PMCID: 5946407
PMID: 29747637
DOI: 10.1186/s12920-018-0364-8
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[…] nalysis after ANOVA. Genome-wide associations were visualized using a software program (R, version 3.4.0; The R Foundation). Regional associations were visualized with the Locus Zoom web tool (http://locuszoom.org/). Moreover, a multiple linear regression model was applied using PLINK to estimate coefficients for testing a possible correlation between brain structure and rs7943454. Age, gender, ed […]

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Sex specific glioma genome wide association study identifies new risk locus at 3p21.31 in females, and finds sex differences in risk at 8q24.21

2018
Sci Rep
PMCID: 5943590
PMID: 29743610
DOI: 10.1038/s41598-018-24580-z
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[…] l, sex-specific effect estimates were generated using stratified logistic regression models. Y chromosome data were analyzed using logistic regression in SNPTEST (Fig. ). Figures were generated using LocusZoom and R 3.3.2 using GenABEL, qqman, and ggplot–. […]

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Genome wide association study in 176,678 Europeans reveals genetic loci for tanning response to sun exposure

2018
Nat Commun
PMCID: 5940788
PMID: 29739929
DOI: 10.1038/s41467-018-04086-y

[…] P value was lower than 5.0 × 10−8. Genome-wide Manhattan and Q–Q plots were generated using the qqman R package (version 0.1.2). Regional Manhattan plots for the associated loci were generated using LocusZoom Standalone. The genotype data from the individuals included in the UKBB data set was used to estimate a more accurate LD structure. […]

library_books

Meta analysis of GWAS on both Chinese and European populations identifies GPR173 as a novel X chromosome susceptibility gene for SLE

2018
PMCID: 5934841
PMID: 29724251
DOI: 10.1186/s13075-018-1590-3

[…] ing based on LD (r2 < 0.3) excluded 39 SNPs from the list, leaving 9 SNPs with potential independent signals (Additional file : Table S3). Among them, SNP rs13440883 showed the most prominent signal. LocusZoom [] was used to plot the regional (± 200 kb) association signal (Additional file : Figure S2). The association of rs13440883 was detected in both Asian and European data, with a slightly high […]

library_books

Mapping genetic variants for cranial vault shape in humans

2018
PLoS One
PMCID: 5919379
PMID: 29698431
DOI: 10.1371/journal.pone.0196148

[…] ical significance.Our meta-analysis revealed genome-wide significant associations at 15p11.2 for MCW (lead SNP: rs2924767, p = 2.11x10-8) and at 17q11.2 for MCL (lead SNP: rs72841279, p < 5.29x10-9). LocusZoom plots for these two loci are shown in . In addition, 16 loci showed suggestive association (p < 5x10-6) with one of the three traits via meta-analysis (Tables and ). Moreover, another 16 co […]

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LocusZoom institution(s)
Department of Mathematics and Statistics, Calvin College, Grand Rapids, MI, USA

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