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Haploview specifications


Unique identifier OMICS_09142
Name Haploview
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Haploview


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Publications for Haploview

Haploview citations


Association of IL17RC and COL6A1 genetic polymorphisms with susceptibility to ossification of the thoracic posterior longitudinal ligament in Chinese patients

PMCID: 5952594
PMID: 29764467
DOI: 10.1186/s13018-018-0817-y

[…] individual variants were in equilibrium at each locus in the population (Hardy-Weinberg equilibrium), as well as the genotypic and allelic distributions. Pairwise LD was calculated as D′ and R2 using Haploview version 4.2. The Pearson’s χ2 test was used to determine the correlation between the variants and the disease based on the odds ratios (ORs) with 95% confidence intervals (95% CI). All stati […]


The IL7RA rs6897932 polymorphism is associated with progression of liver fibrosis in patients with chronic hepatitis C: Repeated measurements design

PLoS One
PMCID: 5942816
PMID: 29742149
DOI: 10.1371/journal.pone.0197115
call_split See protocol

[…] ich can negatively affect the progression of liver disease [].The Statistical Package for the Social Sciences (SPSS) 21.0 software (IBM Corp., Chicago, USA) was used to perform the statistical tests. Haploview 4.2 software was used to evaluate the pairwise linkage disequilibrium (LD). The frequencies of haplotypes were estimated considering the Expectation-Maximization algorithm. PLINK software (h […]


Evaluation of WISP1 as a candidate gene for bone mineral density in the Old Order Amish

Sci Rep
PMCID: 5940677
PMID: 29739999
DOI: 10.1038/s41598-018-25272-4
call_split See protocol

[…] U reference sample phase2. SNPs with Imputation quality score (INFO) ≥30% were considered. Selection of the tagSNPs was performed based on the OOA genotyping data. Using the aggressive tagger mode of Haploview version 4.2 (http://www.broadinstitute.org/haploview/), we selected 58 tagSNPs which cover all common genetic variation within 5 kb upstream and downstream to WISP1 gene (Chr8: 134198282–134 […]


Applications and efficiencies of the first cat 63K DNA array

Sci Rep
PMCID: 5935720
PMID: 29728693
DOI: 10.1038/s41598-018-25438-0

[…] IBD values were obtained using the command–genome using PLINK. For each population independently, r2 was calculated for autosomal markers that exhibited (MAF ≥ 0.05) and analyses were performed using Haploview.Pairwise r2 estimates between autosomal markers on the same chromosome were jointly categorized into distance bins of 50 Kb. The range of distances between markers included in the estimation […]


Genetic variants in the exon region of versican predict survival of patients with resected early stage hepatitis B virus associated hepatocellular carcinoma

PMCID: 5942399
PMID: 29765250
DOI: 10.2147/CMAR.S161906

[…] was estimated using a goodness-of-fit χ2-test with one degree of freedom. The linkage disequilibrium between SNPs of the VCAN gene and the haplotype block were conducted using Gabriel’s algorithm in Haploview version 4.2. For all of these 5 SNPs, 1 reasonable genetic model (dominant, additive, or recessive models) was used. Overall survival (OS) was defined from the date of the hepatectomy to dea […]


Gene based analysis of genes related to neurotrophic pathway suggests association of BDNF and VEGFA with antidepressant treatment response in depressed patients

Sci Rep
PMCID: 5934385
PMID: 29725086
DOI: 10.1038/s41598-018-25529-y
call_split See protocol

[…] yses to investigate whether the treatment-response associated loci were also MDD susceptible loci.All aforementioned analyses were conducted with R version 3.0.2, PLINK version 1. 90b3.37 64-bit, and haploview version 4.1. Additionally, to explore the potential roles of these six SNPs as expression quantitative trait locus (eQTL), we used HaploReg (http://compbio.mit.edu/HaploReg) to search gene r […]


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Haploview institution(s)
Whitehead Institute for Biomedical Research Cambridge, MA, USA; MIT Media Lab Cambridge, MA, USA; Broad Institute of Harvard and MIT Cambridge, MA, USA

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