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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B. I. Freedman, P. J. Hicks, M. A. Bostrom, M. E. Comeau, J. Divers, A. J. Bleyer, J. B. Kopp, C. A. Winkler, G. W. Nelson, C. D. Langefeld, et al. Non-muscle myosin heavy chain 9 gene MYH9 associations in African Americans with clinically diagnosed type 2 diabetes mellitus-associated ESRD Nephrol. Dial. Transplant., November 1, 2009; 24(11): 3366 - 3371. [Abstract] [Full Text] [PDF]
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 B. K. Rana, J. Wessel, V. Mahboubi, F. Rao, J. Haeller, J. R. Gayen, E. Eskin, A. M. Valle, M. Das, S. K. Mahata, et al. Natural Variation within the Neuronal Nicotinic Acetylcholine Receptor Cluster on Human Chromosome 15q24: Influence on Heritable Autonomic Traits in Twin Pairs J. Pharmacol. Exp. Ther., November 1, 2009; 331(2): 419 - 428. [Abstract] [Full Text] [PDF]
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P.-a. B. Shih, L. Wang, S. Chiron, G. Wen, C. Nievergelt, M. Mahata, S. Khandrika, F. Rao, M. M. Fung, S. K. Mahata, et al. Peptide YY (PYY) Gene Polymorphisms in the 3'-Untranslated and Proximal Promoter Regions Regulate Cellular Gene Expression and PYY Secretion and Metabolic Syndrome Traits in Vivo J. Clin. Endocrinol. Metab., November 1, 2009; 94(11): 4557 - 4566. [Abstract] [Full Text] [PDF]
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K. Luotola, R. Paakkonen, M. Alanne, T. Lanki, L. Moilanen, I. Surakka, A. Pietila, M. Kahonen, M. S. Nieminen, Y. A. Kesaniemi, et al. Association of Variation in the Interleukin-1 Gene Family with Diabetes and Glucose Homeostasis J. Clin. Endocrinol. Metab., November 1, 2009; 94(11): 4575 - 4583. [Abstract] [Full Text] [PDF]
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L. Chen, G. Davey Smith, D. M. Evans, A. Cox, D. A. Lawlor, J. Donovan, W. Yuan, I. N. M. Day, R. M. Martin, A. Lane, et al. Genetic Variants in the Vitamin D Receptor Are Associated with Advanced Prostate Cancer at Diagnosis: Findings from the Prostate Testing for Cancer and Treatment Study and a Systematic Review Cancer Epidemiol. Biomarkers Prev., November 1, 2009; 18(11): 2874 - 2881. [Abstract] [Full Text] [PDF]
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J. S. Kwon, Y. H. Joo, H. J. Nam, M. Lim, E.-Y. Cho, M. H. Jung, J.-S. Choi, B. Kim, D.-H. Kang, S. Oh, et al. Association of the Glutamate Transporter Gene SLC1A1 With Atypical Antipsychotics-Induced Obsessive-compulsive Symptoms Arch Gen Psychiatry, November 1, 2009; 66(11): 1233 - 1241. [Abstract] [Full Text] [PDF]
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 Y.-Y. Teo, X. Sim, R. T.H. Ong, A. K.S. Tan, J. Chen, E. Tantoso, K. S. Small, C.-S. Ku, E. J.D. Lee, M. Seielstad, et al. Singapore Genome Variation Project: A haplotype map of three Southeast Asian populations Genome Res., November 1, 2009; 19(11): 2154 - 2162. [Abstract] [Full Text] [PDF]
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 F.-I Hsieh, W.-C. Lo, H.-J. Lin, Y.-C. Hsieh, L.-M. Lien, C.-H. Bai, H.-P. Tseng, and H.-Y. Chiou Significant Synergistic Effect of Peroxisome Proliferator-Activated Receptor {gamma} C-2821T and Diabetes on the Risk of Ischemic Stroke Diabetes Care, November 1, 2009; 32(11): 2033 - 2035. [Abstract] [Full Text] [PDF]
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A. Eberlein, A. Takasuga, K. Setoguchi, R. Pfuhl, K. Flisikowski, R. Fries, N. Klopp, R. Furbass, R. Weikard, and C. Kuhn Dissection of Genetic Factors Modulating Fetal Growth in Cattle Indicates a Substantial Role of the Non-SMC Condensin I Complex, Subunit G (NCAPG) Gene Genetics, November 1, 2009; 183(3): 951 - 964. [Abstract] [Full Text] [PDF]
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 U Huffmeier, J Lascorz, T Becker, F Schurmeier-Horst, A Magener, A B Ekici, S Endele, C T Thiel, S Thoma-Uszynski, R Mossner, et al. Characterisation of psoriasis susceptibility locus 6 (PSORS6) in patients with early onset psoriasis and evidence for interaction with PSORS1 J. Med. Genet., November 1, 2009; 46(11): 736 - 744. [Abstract] [Full Text] [PDF]
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Y. Xue, X. Zhang, N. Huang, A. Daly, C. J. Gillson, D. G. MacArthur, B. Yngvadottir, A. C. Nica, C. Woodwark, Y. Chen, et al. Population Differentiation as an Indicator of Recent Positive Selection in Humans: An Empirical Evaluation Genetics, November 1, 2009; 183(3): 1065 - 1077. [Abstract] [Full Text] [PDF]
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D. A. Brown, F. Lindmark, P. Stattin, K. Balter, H.-O. Adami, S. L. Zheng, J. Xu, W. B. Isaacs, H. Gronberg, S. N. Breit, et al. Macrophage Inhibitory Cytokine 1: A New Prognostic Marker in Prostate Cancer Clin. Cancer Res., November 1, 2009; 15(21): 6658 - 6664. [Abstract] [Full Text] [PDF]
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 A-K Abelson, A M Delgado-Vega, S V Kozyrev, E Sanchez, R Velazquez-Cruz, N Eriksson, J Wojcik, M V P Linga Reddy, G Lima, S D'Alfonso, et al. STAT4 associates with systemic lupus erythematosus through two independent effects that correlate with gene expression and act additively with IRF5 to increase risk Ann Rheum Dis, November 1, 2009; 68(11): 1746 - 1753. [Abstract] [Full Text] [PDF]
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M. Ogorelkova, A. Navarro, F. Vivarelli, A. Ramirez-Soriano, and X. Estivill Positive Selection and Gene Conversion Drive the Evolution of a Brain-Expressed snoRNAs Cluster Mol. Biol. Evol., November 1, 2009; 26(11): 2563 - 2571. [Abstract] [Full Text] [PDF]
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H. J. Edenberg and Y. Liu Laboratory Methods for High-Throughput Genotyping CSH Protocols, November 1, 2009; 2009(11): pdb.top62 - pdb.top62. [Abstract] [Full Text]
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 M. Iijima, M. Tomita, S. Morozumi, Y. Kawagashira, T. Nakamura, H. Koike, M. Katsuno, N. Hattori, F. Tanaka, M. Yamamoto, et al. Single nucleotide polymorphism of TAG-1 influences IVIg responsiveness of Japanese patients with CIDP Neurology, October 27, 2009; 73(17): 1348 - 1352. [Abstract] [Full Text] [PDF]
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A. Hussein, E. Askar, M. Elsaeid, and F. Schaefer Functional polymorphisms in transforming growth factor-beta-1 (TGF{beta}-1) and vascular endothelial growth factor (VEGF) genes modify risk of renal parenchymal scarring following childhood urinary tract infection Nephrol. Dial. Transplant., October 26, 2009; (2009) gfp532v1. [Abstract] [Full Text] [PDF]
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 D. Voora, S. H. Shah, I. Spasojevic, S. Ali, C. R. Reed, B. A. Salisbury, and G. S. Ginsburg The SLCO1B1*5 genetic variant is associated with statin-induced side effects. J. Am. Coll. Cardiol., October 20, 2009; 54(17): 1609 - 1616. [Abstract] [Full Text] [PDF]
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M. R. Akbari, R. Malekzadeh, R. Shakeri, D. Nasrollahzadeh, M. Foumani, Y. Sun, A. Pourshams, A. Sadjadi, E. Jafari, M. Sotoudeh, et al. Candidate Gene Association Study of Esophageal Squamous Cell Carcinoma in a High-Risk Region in Iran Cancer Res., October 15, 2009; 69(20): 7994 - 8000. [Abstract] [Full Text] [PDF]
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 S. Cha, I. Koo, B. L. Park, S. Jeong, S. M. Choi, K. S. Kim, H. D. Shin, and J. Y. Kim Genetic Effects of FTO and MC4R Polymorphisms on Body Mass in Constitutional Types Evid. Based Complement. Altern. Med., October 11, 2009; (2009) nep162v1. [Abstract] [Full Text] [PDF]
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A. D. Johnson Single-Nucleotide Polymorphism Bioinformatics: A Comprehensive Review of Resources Circ Cardiovasc Genet, October 1, 2009; 2(5): 530 - 536. [Full Text] [PDF]
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M. T. Vuong, S. Lundberg, I. Gunnarsson, L. Wramner, M. Seddighzadeh, M. Hahn-Zoric, A. Fernstrom, L. A Hanson, L. T. Do, S. H. Jacobson, et al. Genetic variation in the transforming growth factor-{beta}1 gene is associated with susceptibility to IgA nephropathy Nephrol. Dial. Transplant., October 1, 2009; 24(10): 3061 - 3067. [Abstract] [Full Text] [PDF]
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 J. Y. Dai, M. Leblanc, N. L. Smith, B. Psaty, and C. Kooperberg SHARE: an adaptive algorithm to select the most informative set of SNPs for candidate genetic association Biostat., October 1, 2009; 10(4): 680 - 693. [Abstract] [Full Text] [PDF]
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Y.-H. Shu, J. Hartiala, A. H. Xiang, E. Trigo, J. M. Lawrence, H. Allayee, T. A. Buchanan, N. Bottini, and R. M. Watanabe Evidence for Sex-Specific Associations between Variation in Acid Phosphatase Locus 1 (ACP1) and Insulin Sensitivity in Mexican-Americans J. Clin. Endocrinol. Metab., October 1, 2009; 94(10): 4094 - 4102. [Abstract] [Full Text] [PDF]
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S. C. Body, C. D. Collard, S. K. Shernan, A. A. Fox, K.-Y. Liu, M. D. Ritchie, T. E. Perry, J. D. Muehlschlegel, S. Aranki, B. S. Donahue, et al. Variation in the 4q25 Chromosomal Locus Predicts Atrial Fibrillation After Coronary Artery Bypass Graft Surgery Circ Cardiovasc Genet, October 1, 2009; 2(5): 499 - 506. [Abstract] [Full Text] [PDF]
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I. Iatan, Z. Dastani, R. Do, D. Weissglas-Volkov, I. Ruel, J. C. Lee, A. Huertas-Vazquez, M.-R. Taskinen, A. Prat, N. G. Seidah, et al. Genetic Variation at the Proprotein Convertase Subtilisin/Kexin Type 5 Gene Modulates High-Density Lipoprotein Cholesterol Levels Circ Cardiovasc Genet, October 1, 2009; 2(5): 467 - 475. [Abstract] [Full Text] [PDF]
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S. Weinsheimer, H. Kim, L. Pawlikowska, Y. Chen, M. T. Lawton, S. Sidney, P.-Y. Kwok, C. E. McCulloch, and W. L. Young EPHB4 Gene Polymorphisms and Risk of Intracranial Hemorrhage in Patients With Brain Arteriovenous Malformations Circ Cardiovasc Genet, October 1, 2009; 2(5): 476 - 482. [Abstract] [Full Text] [PDF]
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E. L. Barry, L. B. Sansbury, M. V. Grau, I. U. Ali, S. Tsang, D. J. Munroe, D. J. Ahnen, R. S. Sandler, F. Saibil, J. Gui, et al. Cyclooxygenase-2 Polymorphisms, Aspirin Treatment, and Risk for Colorectal Adenoma Recurrence--Data from a Randomized Clinical Trial Cancer Epidemiol. Biomarkers Prev., October 1, 2009; 18(10): 2726 - 2733. [Abstract] [Full Text] [PDF]
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