Computational protocol: Genetic Polymorphisms in ZFHX3 Are Associated with Atrial Fibrillation in a Chinese Han Population

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Protocol publication

[…] We first used public HapMap SNP database (phase II + III Feb 09, on NCBI B36 assembly, dbSNP b126) to search SNPs that localized within the gene region of ZFHX3 (including 10 kb up-stream region of the gene), with MAF≥0.05 in Chinese Han population (CHB). Then, a web-based analysis tool was used to predict the function of these SNPs (http://snpinfo.niehs.nih.gov/snpinfo/snpfunc.htm). After function prediction analysis, a total of 9 potentially functional SNPs were selected. Using the Haploview 4.2 software, linkage disequilibrium (LD) analysis with an r2≥0.8 was further applied to filter these functional SNPs and 7 (rs12596992, rs13336412, rs16971312, rs16971436, rs17680796, rs6499600, rs8049936) of which were remained. Additionally, previously reported single nucleotide polymorphism (SNP) rs2106261 in ZFHX3 was selected as well for this study. As a result, 8 loci were finally determined to perform genotyping. […]

Pipeline specifications

Software tools SNPinfo, Haploview
Databases dbSNP
Application GWAS
Organisms Homo sapiens
Diseases Coronary Artery Disease