Basic Info

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Basic Information for the SNP-ceRNA event

Variation

rs60056002  chr11:2692318(T/C)

lncRNA

KCNQ1OT1 ( ENSG00000269821)

miRNA

hsa-miR-339-5p (MIMAT0000764)

mRNA

BACE1 (ENSG00000186318)

Population

YRI

FDR

3.36E-8

Reported as biomarkers
1

Circulating
3

Drug resistent
8

Survival

Binding Info

Altered binding affnity between reference and alternative allele

miRanda reference allele   (loss)
                                           
                       NA                  
                                           
                         
            NA
miRanda alternative allele   (loss)
                                           
                       NA                  
                                           
                         
            NA
TargetScan reference allele   (loss)
                                           
                       NA                  
                                           
                         
            NA
TargetScan alternative allele   (loss)
                                           
                       NA                  
                                           
                         
            NA
RNAhybrid reference allele   (gain)
miRNA  3' G   U  AGG                       5' hsa-miR-339-5p
           CAC CG        ACCUCC   UGUCCCU    
           GUG GC        UGGAGG   GCAGGGA    
target 5' A      AAUAGGGA      GAA       A 3' KCNQ1OT1
Start: 51  End: 71
Energy: -31.9 kcal/mol
Align Score: 0.000366
RNAhybrid alternative allele   (gain)
miRNA  3' G   U  AGG                       5' hsa-miR-339-5p
           CAC CG        ACCUCC   UGUCCCU    
           GUG GC        UGGAGG   GCAGGGA    
target 5' G      AAUAGGGA      GAA       A 3' KCNQ1OT1
Start: 51  End: 71
Energy: -31.7 kcal/mol
Align Score: 0.000401

Functions

Dysregulated fucntions of SNP-ceRNA event

Hallmarks

Dysregulated hallmarks of SNP-ceRNA event

Network

The KCNQ1OT1-associated ceRNA network which were dysregulated by rs60056002

Related ceRNA network disturbed by SNP

Survival

Survival status of ceRNA interaction

Samples

Samples with different genotypes

Annotations

External Annotation for KCNQ1OT1

LncRNA-associated competing triplets and functions.

Comprehensive experimentally supported associations between lncRNA and human cancer.

An open-source platform for studying the RNA-RNA interactions from CLIP-seq data.

An integrated knowledge database dedicated to non-coding RNAs.

An integrated database of human annotated lncRNA transcripts.

Comprehensive annotations of eukaryotic long non-coding RNAs.



External Annotation for hsa-miR-339-5p

A high quality database of published miRNA sequences and annotation.

A curated miRNA-target database developed by DIANA LAB.

A miRNA-target database by manually filter research articles related to functional studies of miRNAs.

A comprehensive of microRNA diversity, expression profiles, target relationships, and various supporting tools.



External Annotation for BACE1

Information on all annotated and predicted human genes.

Gene nomenclature, gene families and associated resources (genomic, proteomic, phenotypic information).

Genome browser for vertebrate genomes.

An annotated collection of all publicly available DNA sequences.



External Annotation for variation: rs60056002

A comprehensive, authoritative compendium of human genes and genetic phenotypes.

A database of human single nucleotide variations, microsatellites, and small-scale insertions and deletions

The catalogue of somatic mutations in cancer.