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MirSNP, a database of polymorphisms altering miRNA target sites, identifies miRNA-related SNPs in GWAS SNPs and eQTLs
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MirSNP, a database of polymorphisms altering miRNA target sites, identifies miRNA-related SNPs in GWAS SNPs and eQTLs
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Journal Article
MirSNP, a database of polymorphisms altering miRNA target sites, identifies miRNA-related SNPs in GWAS SNPs and eQTLs
2012
Overview
Background
Numerous single nucleotide polymorphisms (SNPs) associated with complex diseases have been identified by genome-wide association studies (GWAS) and expression quantitative trait loci (eQTLs) studies. However, few of these SNPs have explicit biological functions. Recent studies indicated that the SNPs within the 3’UTR regions of susceptibility genes could affect complex traits/diseases by affecting the function of miRNAs. These 3’UTR SNPs are functional candidates and therefore of interest to GWAS and eQTL researchers.
Description
We developed a publicly available online database, MirSNP (
http://cmbi.bjmu.edu.cn/mirsnp
), which is a collection of human SNPs in predicted miRNA-mRNA binding sites. We identified 414,510 SNPs that might affect miRNA-mRNA binding. Annotations were added to these SNPs to predict whether a SNP within the target site would decrease/break or enhance/create an miRNA-mRNA binding site. By applying MirSNP database to three brain eQTL data sets, we identified four unreported SNPs (rs3087822, rs13042, rs1058381, and rs1058398), which might affect miRNA binding and thus affect the expression of their host genes in the brain. We also applied the MirSNP database to our GWAS for schizophrenia: seven predicted miRNA-related SNPs (
p
< 0.0001) were found in the schizophrenia GWAS. Our findings identified the possible functions of these SNP loci, and provide the basis for subsequent functional research.
Conclusion
MirSNP could identify the putative miRNA-related SNPs from GWAS and eQTLs researches and provide the direction for subsequent functional researches.
Publisher
BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
Subject
3' Untranslated Regions - genetics
/ Animal Genetics and Genomics
/ Biomedical and Life Sciences
/ Disease
/ Expression quantitative trait loci (eQTLs)
/ Genetics
/ Genome-Wide Association Study
/ Genome-wide association study (GWAS)
/ Genomes
/ Genomics
/ Humans
/ Internet
/ Microbial Genetics and Genomics
/ MicroRNA
/ MirSNP
/ Polymorphism, Single Nucleotide
/ Science
/ Single nucleotide polymorphism (SNP)
/ Single nucleotide polymorphisms
/ Structured Query Language-SQL
/ Studies
