Bioinformatics Advance Access originally published online on August 5, 2004
Bioinformatics 2005 21(2):263-265; doi:10.1093/bioinformatics/bth457
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Bioinformatics vol. 21 issue 2 © Oxford University Press 2005; all rights reserved.
Haploview: analysis and visualization of LD and haplotype maps
1 Whitehead Institute for Biomedical Research Cambridge, MA 02142, USA
2 MIT Media Lab Cambridge, MA 02139, USA
3 Broad Institute of Harvard and MIT Cambridge, MA, USA
*To whom correspondence should be addressed.
Summary: Research over the last few years has revealed significant haplotype structure in the human genome. The characterization of these patterns, particularly in the context of medical genetic association studies, is becoming a routine research activity. Haploview is a software package that provides computation of linkage disequilibrium statistics and population haplotype patterns from primary genotype data in a visually appealing and interactive interface.
Availability: http://www.broad.mit.edu/mpg/haploview/
Contact: jcbarret{at}broad.mit.edu
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|
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|
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|
|
|
|
 |
|
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|
|
|
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 |
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|
|
|
|
 |
|
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|
|
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|
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|
|
|
|
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|
|
|
|
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|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
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|
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|
|
|
|
 |
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
 G. Atzmon, T. I. Pollin, J. Crandall, K. Tanner, C. B. Schechter, P. E. Scherer, M. Rincon, G. Siegel, M. Katz, R. B. Lipton, et al. Adiponectin Levels and Genotype: A Potential Regulator of Life Span in Humans J. Gerontol. A Biol. Sci. Med. Sci., May 1, 2008; 63(5): 447 - 453. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. M. Mercader, E. Saus, Z. Aguera, M. Bayes, C. Boni, A. Carreras, E. Cellini, R. de Cid, M. Dierssen, G. Escaramis, et al. Association of NTRK3 and its interaction with NGF suggest an altered cross-regulation of the neurotrophin signaling pathway in eating disorders Hum. Mol. Genet., May 1, 2008; 17(9): 1234 - 1244. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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|
|
|
|
|
|
J.-k. Wang, Y. Li, and B. Su A common SNP of MCPH1 is associated with cranial volume variation in Chinese population Hum. Mol. Genet., May 1, 2008; 17(9): 1329 - 1335. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Feng, A. Vetro, E. Kiss, K. Kapornai, G. Daroczi, L. Mayer, Z. Tamas, I. Baji, J. Gadoros, N. King, et al. Association of the Neurotrophic Tyrosine Kinase Receptor 3 (NTRK3) Gene and Childhood-Onset Mood Disorders Am J Psychiatry, May 1, 2008; 165(5): 610 - 616. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
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|
|
|
|
 |
|
 A. Salhi, V. Rodrigues Jr., F. Santoro, H. Dessein, A. Romano, L. R. Castellano, M. Sertorio, S. Rafati, C. Chevillard, A. Prata, et al. Immunological and Genetic Evidence for a Crucial Role of IL-10 in Cutaneous Lesions in Humans Infected with Leishmania braziliensis J. Immunol., May 1, 2008; 180(9): 6139 - 6148. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. Kristiansson, E. Ilveskoski, T. Lehtimaki, L. Peltonen, M. Perola, and P. J. Karhunen Association Analysis of Allelic Variants of USF1 in Coronary Atherosclerosis Arterioscler. Thromb. Vasc. Biol., May 1, 2008; 28(5): 983 - 989. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
 S. Leng, C. A. Stidley, R. Willink, A. Bernauer, K. Do, M. A. Picchi, X. Sheng, M. A. Frasco, D. Van Den Berg, F. D. Gilliland, et al. Double-Strand Break Damage and Associated DNA Repair Genes Predispose Smokers to Gene Methylation Cancer Res., April 15, 2008; 68(8): 3049 - 3056. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
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|
|
|
|
 |
|
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|
|
|
|
 |
|
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|
|
|
|
 |
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
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