Computational protocol: The rs6771157 C/G polymorphism in SCN10A is associated with the risk of 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 SCN10A (including 10 kb upstream of the gene), with MAF (Minor Allele Frequency) ≥ 0.05 in Chinese Han population. 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 six potentially functional SNPs were selected. We conducted linkage disequilibrium (LD) analysis to exclude SNPs with strong LD (r2 ≥ 0.8), then three (rs9827941, rs7630989, and rs6771157) functional SNPs were selected for further genotyping. [...] The comparisons of clinical characteristic differences between cases and controls were identified using Student’s t test for continuous variables and the χ2 test for categorical variables. The deviation of genotype distribution from Hardy-Weinberg equilibrium was tested by χ2 test in the control group. ORs and 95% CIs were calculated to assess the relationships between the SNPs and the risk of AF using logistic regression. The heterogeneity of associations among subgroups was evaluated using the χ2-based Q-test. All statistical analyses were performed with STATA 12.0 software (Stata Corp., College Station, TX, USA). P < 0.05 was the criterion of statistical significance and all statistical tests were two-tailed. LD analysis was applied by using Haploview 4.2 software. […]

Pipeline specifications

Software tools SNPinfo, Haploview
Databases dbSNP
Application GWAS