MirSNP

A collection of human SNPs in predicted miRNA target sites


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Single search:
Gene: Refgene name
mRNA: mRNA id
SNP: e.g. rs6919 or 6919
miRNA:

Display: Binding map

Display the miRNA-mRNA binding map for different alleles

Filter: CEU HCB JPT YRI

The results is filtered by MAF of different populations (MAF > 0.01)

Batch search:
Gene: Example file
mRNA: Example file
SNP: Example file

Upload Gene/mRNA/SNP list in a text file.

Filter: MAF

Filter the results by MAF (MAF > 0.01 in at least one population of four) and display MAF information of four populations in output

Query disease & trait associated SNPs:

Example file

Upload SNP list in a text file.

Analysis: Consider linkaged SNPs (R-square > 0.8)
CEU HCB+JPT YRI Four populations

Query not only the submitted SNPs but also their linkage SNPs (R-square > 0.8 in a specific population)
Data source
SNP:dbSNP135
Altogether 513,249 3'UTR SNPs
miRNA:mirBASE18
Altogether 1,921 mature miRNAs
mRNA:NCBI
Altogether 42,733 mRNAs
LD:HapMap
Phase 2 HapMap data

Prediction Strategies
miRanda software (7-nt seed alignment)

Statistics
Involved Genes: 17,569
Involved mRNAs: 29,273
Involved miRNAs: 1,921
MirSNPs: 414,510
MirSNPs (MAF > 0.01): 32,822
Records: 2,709,054
Records (MAF > 0.01): 227,061

How to cite: MirSNP, a database of polymorphisms altering miRNA target sites, identifies miRNA-related SNPs in GWAS SNPs and eQTLs.

Liu C, Zhang F, Li T, Lu M, Wang L, Yue W*, Zhang D*. BMC Genomics. 2012 Nov 23;13(1):661.

Developed by: Prof. D. Zhang's Lab, Ministry of Health Key Laboratory of Mental Health, Peking University.

Any comments or suggestions, please contact us : chenxingl@bjmu.edu.cn