Computational protocol: A Novel Functional TagSNP Rs7560488 in the DNMT3A1 Promoter Is Associated with Susceptibility to Gastric Cancer by Modulating Promoter Activity

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Protocol publication

[…] The principal hypothesis underlying this experiment was that there are one or more SNPs in the DNMT3A1 promoter regions that are associated with the risk of gastric cancer. Depending on the linkage disequilibrium (LD) structure at a particular locus, tagSNPs may be surrogates for many thousands of other SNPs. We postulate that such tagSNPs are also likely to tag any hitherto identified SNPs in the DNMT3A1 promoter. Thus, we selected the SNPs in the DNMT3A1 promoter region with a minor allele frequency (MAF) of >5% from both the HapMap and dbSNPs databases. To implement potentially functional tagSNP selection, we use data from the International HapMap and the freely web-based tagSNP selection tools to select tagSNPs, and use the TF-search algorithm ( to predict rs7560488 transcription factor (TF) binding site. […]

Pipeline specifications

Software tools SNPinfo, TFSearch
Application GWAS
Diseases Neoplasms, Stomach Neoplasms