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MirSNP, a database of polymorphisms altering miRNA target sites, identifies miRNA-related SNPs in GWAS SNPs and eQTLs

Chenxing Liu12, Fuquan Zhang12, Tingting Li45, Ming Lu4, Lifang Wang12, Weihua Yue12* and Dai Zhang123*

Author Affiliations

1 Institute of Mental Health, Peking University, 51 Hua Yuan Bei Road, Beijing 100191, People’s Republic of China

2 Key Laboratory of Mental Health, Ministry of Health (Peking University), Beijing, 100191, China

3 Peking-Tsinghua Center for Life Sciences, Beijing 100871, China

4 Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China

5 Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China

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BMC Genomics 2012, 13:661  doi:10.1186/1471-2164-13-661

Published: 23 November 2012



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.


We developed a publicly available online database, MirSNP ( webcite), 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.


MirSNP could identify the putative miRNA-related SNPs from GWAS and eQTLs researches and provide the direction for subsequent functional researches.

microRNA; Single nucleotide polymorphism (SNP); Genome-wide association study (GWAS); Expression quantitative trait loci (eQTLs); MirSNP