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Haplotter specifications

Information


Unique identifier OMICS_08600
Name Haplotter
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Maintainer


  • person_outline Jonathan K. Pritchard

Publication for Haplotter

Haplotter citations

 (47)
library_books

Neuregulin signaling pathway in smoking behavior

2017
PMCID: 5611747
PMID: 28892072
DOI: 10.1038/tp.2017.183

[…] 0.93), and only two SNPs had an info score <0.7. NRG3 SNP rs11192578 showed mild LD with neighboring SNPs plausibly explained by suggestive evidence of positive selection (iHS score 1.7 obtained from Haplotter (haplotter.uchicago.edu) and low minor allele frequency (MAF=0.04) in our sample. ERBB4 SNP rs13385826 (showing association with ND diagnosis) appears to be an orphan signal with no support […]

library_books

Single trait and multi trait genome wide association analyses identify novel loci for blood pressure in African ancestry populations

2017
PLoS Genet
PMCID: 5446189
PMID: 28498854
DOI: 10.1371/journal.pgen.1006728

[…] To evaluate population differentiation and natural selection, using Haplotter,[] we calculated the integrated haplotype score (iHS) in five cohorts of CARe so that we could measure the amount of extended haplotype homozygosity (http://coruscant.itmat.upenn.edu/whamm/i […]

library_books

OSBPL10, RXRA and lipid metabolism confer African ancestry protection against dengue haemorrhagic fever in admixed Cubans

2017
PLoS Pathog
PMCID: 5344536
PMID: 28241052
DOI: 10.1371/journal.ppat.1006220

[…] was used for gene set enrichment analysis of the LXR/RXR activation pathway in the Thai dengue dataset [] by considering three sets of genes: lipid metabolism, LXR/RXR activation and NF-kB activation.Haplotter database (http://haplotter.uchicago.edu/) was used to explore recent positive selection through iHS measure (detects selective sweeps at 50–80% frequencies). By using the selscan package [], […]

library_books

Evidence of Polygenic Adaptation in the Systems Genetics of Anthropometric Traits

2016
PLoS One
PMCID: 4990182
PMID: 27537407
DOI: 10.1371/journal.pone.0160654

[…] AS on European ancestry populations, we used the iHS data based on the HapMap Phase 2 CEU (Utah residents with Northern and Western European ancestry from the CEPH collection) population available in Haplotter database []. Previous studies used |iHS| > 1.5 as suggestive evidence for natural selection [–], in agreement with a recent simulation analysis that indicated |iHS| > 2.0 is too stringent a […]

library_books

Ancient Haplotypes at the 15q24.2 Microdeletion Region Are Linked to Brain Expression of MAN2C1 and Children's Intelligence

2016
PLoS One
PMCID: 4927142
PMID: 27355585
DOI: 10.1371/journal.pone.0157739

[…] N2 and O2, rs4462560 and rs9635320, respectively, showed significant signals of selection by iHS measures (|iHS|>2) in YRI (iHS in rs4462560 = 3.008 and iHS in rs9635320 = -3.822) as reported in the haplotter database (http://haplotter.uchicago.edu/instruction.html) []. We could not eliminate genetic drift as a potential driver of heterozygosities of M2 and P2 haplotypes nor in the FST values in […]

library_books

Discovery of Genetic Variation on Chromosome 5q22 Associated with Mortality in Heart Failure

2016
PLoS Genet
PMCID: 4858216
PMID: 27149122
DOI: 10.1371/journal.pgen.1006034

[…] [], based on allele frequencies in HapMap stage II as also previously described []. The integrated haplotype score (iHS) was calculated from HapMap stage II data as described by Voight et al (http://haplotter.uchicago.edu/) []. Allele frequency distributions in HGDP populations were visualized using the HGDP selection browser (http://hgdp.uchicago.edu/) []. […]

Citations

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Haplotter institution(s)
Department of Human Genetics, University of Chicago, Chicago, IL, USA

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