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Literature DB >> 18974171

SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap.

Andrew D Johnson¹, Robert E Handsaker, Sara L Pulit, Marcia M Nizzari, Christopher J O'Donnell, Paul I W de Bakker.

Abstract

SUMMARY: The interpretation of genome-wide association results is confounded by linkage disequilibrium between nearby alleles. We have developed a flexible bioinformatics query tool for single-nucleotide polymorphisms (SNPs) to identify and to annotate nearby SNPs in linkage disequilibrium (proxies) based on HapMap. By offering functionality to generate graphical plots for these data, the SNAP server will facilitate interpretation and comparison of genome-wide association study results, and the design of fine-mapping experiments (by delineating genomic regions harboring associated variants and their proxies). AVAILABILITY: SNAP server is available at http://www.broad.mit.edu/mpg/snap/.

Entities: Gene

Mesh：

Year: 2008 PMID： 18974171 PMCID： PMC2720775 DOI： 10.1093/bioinformatics/btn564

Source DB: PubMed Journal: Bioinformatics ISSN： 1367-4803 Impact factor: 6.937

9 in total

1. Haploview: analysis and visualization of LD and haplotype maps.

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Journal: Bioinformatics Date: 2004-08-05 Impact factor: 6.937

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Authors: Ted Liefeld; Michael Reich; Joshua Gould; Peili Zhang; Pablo Tamayo; Jill P Mesirov
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Journal: Science Date: 2007-05-03 Impact factor: 47.728

Review 5. Genome-wide association studies for complex traits: consensus, uncertainty and challenges.

Authors: Mark I McCarthy; Gonçalo R Abecasis; Lon R Cardon; David B Goldstein; Julian Little; John P A Ioannidis; Joel N Hirschhorn
Journal: Nat Rev Genet Date: 2008-05 Impact factor: 53.242

6. A common allele on chromosome 9 associated with coronary heart disease.

Authors: Ruth McPherson; Alexander Pertsemlidis; Nihan Kavaslar; Alexandre Stewart; Robert Roberts; David R Cox; David A Hinds; Len A Pennacchio; Anne Tybjaerg-Hansen; Aaron R Folsom; Eric Boerwinkle; Helen H Hobbs; Jonathan C Cohen
Journal: Science Date: 2007-05-03 Impact factor: 47.728

7. Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels.

Authors: Richa Saxena; Benjamin F Voight; Valeriya Lyssenko; Noël P Burtt; Paul I W de Bakker; Hong Chen; Jeffrey J Roix; Sekar Kathiresan; Joel N Hirschhorn; Mark J Daly; Thomas E Hughes; Leif Groop; David Altshuler; Peter Almgren; Jose C Florez; Joanne Meyer; Kristin Ardlie; Kristina Bengtsson Boström; Bo Isomaa; Guillaume Lettre; Ulf Lindblad; Helen N Lyon; Olle Melander; Christopher Newton-Cheh; Peter Nilsson; Marju Orho-Melander; Lennart Råstam; Elizabeth K Speliotes; Marja-Riitta Taskinen; Tiinamaija Tuomi; Candace Guiducci; Anna Berglund; Joyce Carlson; Lauren Gianniny; Rachel Hackett; Liselotte Hall; Johan Holmkvist; Esa Laurila; Marketa Sjögren; Maria Sterner; Aarti Surti; Margareta Svensson; Malin Svensson; Ryan Tewhey; Brendan Blumenstiel; Melissa Parkin; Matthew Defelice; Rachel Barry; Wendy Brodeur; Jody Camarata; Nancy Chia; Mary Fava; John Gibbons; Bob Handsaker; Claire Healy; Kieu Nguyen; Casey Gates; Carrie Sougnez; Diane Gage; Marcia Nizzari; Stacey B Gabriel; Gung-Wei Chirn; Qicheng Ma; Hemang Parikh; Delwood Richardson; Darrell Ricke; Shaun Purcell
Journal: Science Date: 2007-04-26 Impact factor: 47.728

8. A second generation human haplotype map of over 3.1 million SNPs.

Authors: Kelly A Frazer; Dennis G Ballinger; David R Cox; David A Hinds; Laura L Stuve; Richard A Gibbs; John W Belmont; Andrew Boudreau; Paul Hardenbol; Suzanne M Leal; Shiran Pasternak; David A Wheeler; Thomas D Willis; Fuli Yu; Huanming Yang; Changqing Zeng; Yang Gao; Haoran Hu; Weitao Hu; Chaohua Li; Wei Lin; Siqi Liu; Hao Pan; Xiaoli Tang; Jian Wang; Wei Wang; Jun Yu; Bo Zhang; Qingrun Zhang; Hongbin Zhao; Hui Zhao; Jun Zhou; Stacey B Gabriel; Rachel Barry; Brendan Blumenstiel; Amy Camargo; Matthew Defelice; Maura Faggart; Mary Goyette; Supriya Gupta; Jamie Moore; Huy Nguyen; Robert C Onofrio; Melissa Parkin; Jessica Roy; Erich Stahl; Ellen Winchester; Liuda Ziaugra; David Altshuler; Yan Shen; Zhijian Yao; Wei Huang; Xun Chu; Yungang He; Li Jin; Yangfan Liu; Yayun Shen; Weiwei Sun; Haifeng Wang; Yi Wang; Ying Wang; Xiaoyan Xiong; Liang Xu; Mary M Y Waye; Stephen K W Tsui; Hong Xue; J Tze-Fei Wong; Luana M Galver; Jian-Bing Fan; Kevin Gunderson; Sarah S Murray; Arnold R Oliphant; Mark S Chee; Alexandre Montpetit; Fanny Chagnon; Vincent Ferretti; Martin Leboeuf; Jean-François Olivier; Michael S Phillips; Stéphanie Roumy; Clémentine Sallée; Andrei Verner; Thomas J Hudson; Pui-Yan Kwok; Dongmei Cai; Daniel C Koboldt; Raymond D Miller; Ludmila Pawlikowska; Patricia Taillon-Miller; Ming Xiao; Lap-Chee Tsui; William Mak; You Qiang Song; Paul K H Tam; Yusuke Nakamura; Takahisa Kawaguchi; Takuya Kitamoto; Takashi Morizono; Atsushi Nagashima; Yozo Ohnishi; Akihiro Sekine; Toshihiro Tanaka; Tatsuhiko Tsunoda; Panos Deloukas; Christine P Bird; Marcos Delgado; Emmanouil T Dermitzakis; Rhian Gwilliam; Sarah Hunt; Jonathan Morrison; Don Powell; Barbara E Stranger; Pamela Whittaker; David R Bentley; Mark J Daly; Paul I W de Bakker; Jeff Barrett; Yves R Chretien; Julian Maller; Steve McCarroll; Nick Patterson; Itsik Pe'er; Alkes Price; Shaun Purcell; Daniel J Richter; Pardis Sabeti; Richa Saxena; Stephen F Schaffner; Pak C Sham; Patrick Varilly; David Altshuler; Lincoln D Stein; Lalitha Krishnan; Albert Vernon Smith; Marcela K Tello-Ruiz; Gudmundur A Thorisson; Aravinda Chakravarti; Peter E Chen; David J Cutler; Carl S Kashuk; Shin Lin; Gonçalo R Abecasis; Weihua Guan; Yun Li; Heather M Munro; Zhaohui Steve Qin; Daryl J Thomas; Gilean McVean; Adam Auton; Leonardo Bottolo; Niall Cardin; Susana Eyheramendy; Colin Freeman; Jonathan Marchini; Simon Myers; Chris Spencer; Matthew Stephens; Peter Donnelly; Lon R Cardon; Geraldine Clarke; David M Evans; Andrew P Morris; Bruce S Weir; Tatsuhiko Tsunoda; James C Mullikin; Stephen T Sherry; Michael Feolo; Andrew Skol; Houcan Zhang; Changqing Zeng; Hui Zhao; Ichiro Matsuda; Yoshimitsu Fukushima; Darryl R Macer; Eiko Suda; Charles N Rotimi; Clement A Adebamowo; Ike Ajayi; Toyin Aniagwu; Patricia A Marshall; Chibuzor Nkwodimmah; Charmaine D M Royal; Mark F Leppert; Missy Dixon; Andy Peiffer; Renzong Qiu; Alastair Kent; Kazuto Kato; Norio Niikawa; Isaac F Adewole; Bartha M Knoppers; Morris W Foster; Ellen Wright Clayton; Jessica Watkin; Richard A Gibbs; John W Belmont; Donna Muzny; Lynne Nazareth; Erica Sodergren; George M Weinstock; David A Wheeler; Imtaz Yakub; Stacey B Gabriel; Robert C Onofrio; Daniel J Richter; Liuda Ziaugra; Bruce W Birren; Mark J Daly; David Altshuler; Richard K Wilson; Lucinda L Fulton; Jane Rogers; John Burton; Nigel P Carter; Christopher M Clee; Mark Griffiths; Matthew C Jones; Kirsten McLay; Robert W Plumb; Mark T Ross; Sarah K Sims; David L Willey; Zhu Chen; Hua Han; Le Kang; Martin Godbout; John C Wallenburg; Paul L'Archevêque; Guy Bellemare; Koji Saeki; Hongguang Wang; Daochang An; Hongbo Fu; Qing Li; Zhen Wang; Renwu Wang; Arthur L Holden; Lisa D Brooks; Jean E McEwen; Mark S Guyer; Vivian Ota Wang; Jane L Peterson; Michael Shi; Jack Spiegel; Lawrence M Sung; Lynn F Zacharia; Francis S Collins; Karen Kennedy; Ruth Jamieson; John Stewart
Journal: Nature Date: 2007-10-18 Impact factor: 49.962

9. Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes.

Authors: Eleftheria Zeggini; Laura J Scott; Richa Saxena; Benjamin F Voight; Jonathan L Marchini; Tianle Hu; Paul I W de Bakker; Gonçalo R Abecasis; Peter Almgren; Gitte Andersen; Kristin Ardlie; Kristina Bengtsson Boström; Richard N Bergman; Lori L Bonnycastle; Knut Borch-Johnsen; Noël P Burtt; Hong Chen; Peter S Chines; Mark J Daly; Parimal Deodhar; Chia-Jen Ding; Alex S F Doney; William L Duren; Katherine S Elliott; Michael R Erdos; Timothy M Frayling; Rachel M Freathy; Lauren Gianniny; Harald Grallert; Niels Grarup; Christopher J Groves; Candace Guiducci; Torben Hansen; Christian Herder; Graham A Hitman; Thomas E Hughes; Bo Isomaa; Anne U Jackson; Torben Jørgensen; Augustine Kong; Kari Kubalanza; Finny G Kuruvilla; Johanna Kuusisto; Claudia Langenberg; Hana Lango; Torsten Lauritzen; Yun Li; Cecilia M Lindgren; Valeriya Lyssenko; Amanda F Marvelle; Christa Meisinger; Kristian Midthjell; Karen L Mohlke; Mario A Morken; Andrew D Morris; Narisu Narisu; Peter Nilsson; Katharine R Owen; Colin N A Palmer; Felicity Payne; John R B Perry; Elin Pettersen; Carl Platou; Inga Prokopenko; Lu Qi; Li Qin; Nigel W Rayner; Matthew Rees; Jeffrey J Roix; Anelli Sandbaek; Beverley Shields; Marketa Sjögren; Valgerdur Steinthorsdottir; Heather M Stringham; Amy J Swift; Gudmar Thorleifsson; Unnur Thorsteinsdottir; Nicholas J Timpson; Tiinamaija Tuomi; Jaakko Tuomilehto; Mark Walker; Richard M Watanabe; Michael N Weedon; Cristen J Willer; Thomas Illig; Kristian Hveem; Frank B Hu; Markku Laakso; Kari Stefansson; Oluf Pedersen; Nicholas J Wareham; Inês Barroso; Andrew T Hattersley; Francis S Collins; Leif Groop; Mark I McCarthy; Michael Boehnke; David Altshuler
Journal: Nat Genet Date: 2008-03-30 Impact factor: 38.330

9 in total

796 in total

Review 1. Variation in the lysyl oxidase (LOX) gene is associated with keratoconus in family-based and case-control studies.

Authors: Yelena Bykhovskaya; Xiaohui Li; Irina Epifantseva; Talin Haritunians; David Siscovick; Anthony Aldave; Loretta Szczotka-Flynn; Sudha K Iyengar; Kent D Taylor; Jerome I Rotter; Yaron S Rabinowitz
Journal: Invest Ophthalmol Vis Sci Date: 2012-06-28 Impact factor: 4.799

2. Phenotype specific association of the TGFBR3 locus with nonsyndromic cryptorchidism.

Authors: Julia S Barthold; Yanping Wang; Thomas F Kolon; Claude Kollin; Agneta Nordenskjöld; Alicia Olivant Fisher; T Ernesto Figueroa; Ahmad H BaniHani; Jennifer A Hagerty; Ricardo Gonzalez; Paul H Noh; Rosetta M Chiavacci; Kisha R Harden; Debra J Abrams; Cecilia E Kim; Abigail B Mateson; Alan K Robbins; Jin Li; Robert E Akins; Hakon Hakonarson; Marcella Devoto
Journal: J Urol Date: 2014-10-25 Impact factor: 7.450

3. Genome-wide association study for coronary artery calcification with follow-up in myocardial infarction.

Authors: Christopher J O'Donnell; Maryam Kavousi; Albert V Smith; Sharon L R Kardia; Mary F Feitosa; Shih-Jen Hwang; Yan V Sun; Michael A Province; Thor Aspelund; Abbas Dehghan; Udo Hoffmann; Lawrence F Bielak; Qunyuan Zhang; Gudny Eiriksdottir; Cornelia M van Duijn; Caroline S Fox; Mariza de Andrade; Aldi T Kraja; Sigurdur Sigurdsson; Suzette E Elias-Smale; Joanne M Murabito; Lenore J Launer; Aad van der Lugt; Sekar Kathiresan; Gabriel P Krestin; David M Herrington; Timothy D Howard; Yongmei Liu; Wendy Post; Braxton D Mitchell; Jeffrey R O'Connell; Haiqing Shen; Alan R Shuldiner; David Altshuler; Roberto Elosua; Veikko Salomaa; Stephen M Schwartz; David S Siscovick; Benjamin F Voight; Joshua C Bis; Nicole L Glazer; Bruce M Psaty; Eric Boerwinkle; Gerardo Heiss; Stefan Blankenberg; Tanja Zeller; Philipp S Wild; Renate B Schnabel; Arne Schillert; Andreas Ziegler; Thomas F Münzel; Charles C White; Jerome I Rotter; Michael Nalls; Matthijs Oudkerk; Andrew D Johnson; Anne B Newman; Andre G Uitterlinden; Joseph M Massaro; Julie Cunningham; Tamara B Harris; Albert Hofman; Patricia A Peyser; Ingrid B Borecki; L Adrienne Cupples; Vilmundur Gudnason; Jacqueline C M Witteman
Journal: Circulation Date: 2011-12-05 Impact factor: 29.690

4. Association of COL25A1 with comorbid antisocial personality disorder and substance dependence.

Authors: Dawei Li; Hongyu Zhao; Henry R Kranzler; David Oslin; Raymond F Anton; Lindsay A Farrer; Joel Gelernter
Journal: Biol Psychiatry Date: 2012-01-31 Impact factor: 13.382

5. Pathway analysis of genome-wide association study for bone mineral density.

Authors: Young Ho Lee; Sung Jae Choi; Jong Dae Ji; Gwan Gyu Song
Journal: Mol Biol Rep Date: 2012-04-25 Impact factor: 2.316

6. Possible genetic predisposition to lymphedema after breast cancer.

Authors: Beth Newman; Felicity Lose; Mary-Anne Kedda; Mathias Francois; Kaltin Ferguson; Monika Janda; Patsy Yates; Amanda B Spurdle; Sandra C Hayes
Journal: Lymphat Res Biol Date: 2012-03-09 Impact factor: 2.589

7. Impact of common regulatory single-nucleotide variants on gene expression profiles in whole blood.

Authors: Divya Mehta; Katharina Heim; Christian Herder; Maren Carstensen; Gertrud Eckstein; Claudia Schurmann; Georg Homuth; Matthias Nauck; Uwe Völker; Michael Roden; Thomas Illig; Christian Gieger; Thomas Meitinger; Holger Prokisch
Journal: Eur J Hum Genet Date: 2012-06-13 Impact factor: 4.246

8. Broadening our understanding of the genetics of Juvenile Idiopathic Arthritis (JIA): Interrogation of three dimensional chromatin structures and genetic regulatory elements within JIA-associated risk loci.

Authors: Kaiyu Jiang; Haeja Kessler; Yungki Park; Marc Sudman; Susan D Thompson; James N Jarvis
Journal: PLoS One Date: 2020-07-30 Impact factor: 3.240

9. Genome-wide association study identifies 25 known breast cancer susceptibility loci as risk factors for triple-negative breast cancer.

Authors: Kristen S Purrington; Susan Slager; Diana Eccles; Drakoulis Yannoukakos; Peter A Fasching; Penelope Miron; Jane Carpenter; Jenny Chang-Claude; Nicholas G Martin; Grant W Montgomery; Vessela Kristensen; Hoda Anton-Culver; Paul Goodfellow; William J Tapper; Sajjad Rafiq; Susan M Gerty; Lorraine Durcan; Irene Konstantopoulou; Florentia Fostira; Athanassios Vratimos; Paraskevi Apostolou; Irene Konstanta; Vassiliki Kotoula; Sotiris Lakis; Meletios A Dimopoulos; Dimosthenis Skarlos; Dimitrios Pectasides; George Fountzilas; Matthias W Beckmann; Alexander Hein; Matthias Ruebner; Arif B Ekici; Arndt Hartmann; Ruediger Schulz-Wendtland; Stefan P Renner; Wolfgang Janni; Brigitte Rack; Christoph Scholz; Julia Neugebauer; Ulrich Andergassen; Michael P Lux; Lothar Haeberle; Christine Clarke; Nirmala Pathmanathan; Anja Rudolph; Dieter Flesch-Janys; Stefan Nickels; Janet E Olson; James N Ingle; Curtis Olswold; Seth Slettedahl; Jeanette E Eckel-Passow; S Keith Anderson; Daniel W Visscher; Victoria L Cafourek; Hugues Sicotte; Naresh Prodduturi; Elisabete Weiderpass; Leslie Bernstein; Argyrios Ziogas; Jennifer Ivanovich; Graham G Giles; Laura Baglietto; Melissa Southey; Veli-Matti Kosma; Hans-Peter Fischer; Malcom W R Reed; Simon S Cross; Sandra Deming-Halverson; Martha Shrubsole; Qiuyin Cai; Xiao-Ou Shu; Mary Daly; Joellen Weaver; Eric Ross; Jennifer Klemp; Priyanka Sharma; Diana Torres; Thomas Rüdiger; Heidrun Wölfing; Hans-Ulrich Ulmer; Asta Försti; Thaer Khoury; Shicha Kumar; Robert Pilarski; Charles L Shapiro; Dario Greco; Päivi Heikkilä; Kristiina Aittomäki; Carl Blomqvist; Astrid Irwanto; Jianjun Liu; Vernon Shane Pankratz; Xianshu Wang; Gianluca Severi; Arto Mannermaa; Douglas Easton; Per Hall; Hiltrud Brauch; Angela Cox; Wei Zheng; Andrew K Godwin; Ute Hamann; Christine Ambrosone; Amanda Ewart Toland; Heli Nevanlinna; Celine M Vachon; Fergus J Couch
Journal: Carcinogenesis Date: 2013-12-09 Impact factor: 4.944

10. Genetic modifiers and subtypes in schizophrenia: investigations of age at onset, severity, sex and family history.

Authors: Sarah E Bergen; Colm T O'Dushlaine; Phil H Lee; Ayman H Fanous; Douglas M Ruderfer; Stephan Ripke; Patrick F Sullivan; Jordan W Smoller; Shaun M Purcell; Aiden Corvin
Journal: Schizophr Res Date: 2014-02-26 Impact factor: 4.939