SCAN: SNP and copy number annotation.

Bioinformatics
Eric R GamazonNancy J Cox

Abstract

Genome-wide association studies (GWAS) generate relationships between hundreds of thousands of single nucleotide polymorphisms (SNPs) and complex phenotypes. The contribution of the traditionally overlooked copy number variations (CNVs) to complex traits is also being actively studied. To facilitate the interpretation of the data and the designing of follow-up experimental validations, we have developed a database that enables the sensible prioritization of these variants by combining several approaches, involving not only publicly available physical and functional annotations but also multilocus linkage disequilibrium (LD) annotations as well as annotations of expression quantitative trait loci (eQTLs). For each SNP, the SCAN database provides: (i) summary information from eQTL mapping of HapMap SNPs to gene expression (evaluated by the Affymetrix exon array) in the full set of HapMap CEU (Caucasians from UT, USA) and YRI (Yoruba people from Ibadan, Nigeria) samples; (ii) LD information, in the case of a HapMap SNP, including what genes have variation in strong LD (pairwise or multilocus LD) with the variant and how well the SNP is covered by different high-throughput platforms; (iii) summary information available from public ...Continue Reading

References

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Citations

Nov 10, 2012·Theory in Biosciences = Theorie in Den Biowissenschaften·Hong Li
Apr 14, 2011·European Journal of Human Genetics : EJHG·Brooke L Fridley, Joanna M Biernacka
Aug 15, 2012·Molecular Psychiatry·S E StewartD L Pauls
May 6, 2010·Proceedings of the National Academy of Sciences of the United States of America·Eric R GamazonM Eileen Dolan
Jul 28, 2012·Proceedings of the National Academy of Sciences of the United States of America·Dennis C KoSamuel I Miller
Dec 14, 2011·Briefings in Functional Genomics·Marquis P VawterFabio Macciardi
Dec 3, 2011·Bioinformatics·Yupeng WangRomdhane Rekaya
Dec 16, 2011·Bioinformatics·Kai XiaFred A Wright
Mar 29, 2011·Human Molecular Genetics·Michael A GrassiDan L Nicolae
Dec 16, 2011·Human Molecular Genetics·Yujia WenM Eileen Dolan
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Aug 2, 2013·Human Molecular Genetics·Alan R SandersPablo V Gejman
Jul 6, 2010·Nucleic Acids Research·Kai WangHakon Hakonarson
Mar 11, 2010·Pharmacogenetics and Genomics·Eric R GamazonNancy J Cox
Jun 7, 2011·Pharmacogenetics and Genomics·Yujia WenMary Eileen Dolan
Mar 23, 2012·Pharmacogenetics and Genomics·Uchenna O NjiajuM Eileen Dolan
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Dec 4, 2012·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Heather E WheelerMary Eileen Dolan
Jan 22, 2011·Molecular Cancer Therapeutics·Eric R GamazonRong Stephanie Huang
Sep 22, 2010·BMC Bioinformatics·Amol Carl ShettyMichael E Zwick
Jun 14, 2013·BMC Genomics·Eric R GamazonWanqing Liu
Dec 25, 2012·BMC Oral Health·Xiaojing WangMary L Marazita
Oct 14, 2011·Infectious Agents and Cancer·R Renee ReamsClayton Yates
May 26, 2011·Genome Biology·Eric R GamazonNancy J Cox
Jul 13, 2013·Genome Biology·Anat Kreimer, Itsik Pe'er

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