CandiSNPer: a web tool for the identification of candidate SNPs for causal variants

被引：16

作者：

Schmitt, Armin O. ^{[1
]}

Assmus, Jens ^{[1
]}

Bortfeldt, Ralf H. ^{[1
]}

Brockmann, Gudrun A. ^{[1
]}

机构：

[1] Humboldt Univ, Dept Crop & Anim Sci, D-10115 Berlin, Germany

来源：

BIOINFORMATICS | 2010年 / 26卷 / 07期

关键词：

GENOME-WIDE ASSOCIATION; HAPMAP;

D O I：

10.1093/bioinformatics/btq068

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Human single nucleotide polymorphism (SNP) chips which are used in genome-wide association studies (GWAS) permit the genotyping of up to 4 million SNPs simultaneously. To date, about 1000 human SNPs have been identified as statistically significantly associated with a disease or another trait of interest. The identified SNP is not necessarily the causal variant, but it is rather in linkage disequilibrium (LD) with it. CandiSNPer is a software tool that determines the LD region around a significant SNP from a GWAS. It provides a list with functional annotation and LD values for the SNPs found in the LD region. This list contains not only the SNPs for which genotyping data are available, but all SNPs with rs-IDs, thus increasing the likelihood to include the causal variant. Furthermore, plots showing the LD values are generated. CandiSNPer facilitates the preselection of candidate SNPs for causal variants.

引用

页码：969 / 970

页数：2

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