SMARCC1 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10002809
Fusion event
HBV-SMARCC1 integration
Validated
No
Detection method
HIVID
Data source
Curated
Sample type
Tumor
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Normal
Reported year
2016
PubMed ID
27703150
Virus Sequence
Virus name
HBV
Reference genome
AF090842.1;AB033554.1;AB014381.1;M32138.1;AB032431.1;AB036910.1;AB064310;AY090454.1
Host Sequence
Chromosome
chr3
Cytoband
p21.31
Reference genome
GRCh37/hg19
Start
47714823/47673333 (Hg38)
End
47714823/47673333 (Hg38)
Location type
Intronic
Target gene
SMARCC1
miRNAs that regulate target gene
hsa-mir-1-3p ; hsa-mir-34a-5p ; hsa-mir-98-5p ; hsa-let-7b-5p ; hsa-mir-29b-3p ; hsa-let-7f-5p ; hsa-let-7c-5p ; hsa-mir-320c ; hsa-mir-544a ; hsa-mir-6738-3p ; hsa-mir-570-3p ; hsa-mir-4793-3p ; hsa-mir-3130-3p ; hsa-mir-3140-5p ; hsa-mir-4705 ; hsa-mir-34b-3p
Nearest miRNA
hsa-mir-12127/Upstream/2811352; hsa-let-7g/Downstream/176222;
Nearest TSS
ENST00000440867/Upstream/62535; ENST00000472718/Downstream/5032;
Nearest CpG islands
None/Target, chr3-CpG: 148/Upstream/93692, chr3-CpG: 109/Downstream/108098
Nearest cancer related gene
SMARCC1(TSG, No orient, 0)
Upstream sequence
tggtttgggtgaggggtgaggggtgagggtgagggttagggttaggggttagggttagggttagggttagggttagggatgtgggtgagggtgaggatga
Downstream sequence
ggagactgcgccaccgcactccagcttgggcgacagagcgagactctgtctcaaaaaaaaaaGGGTGGGGGGGgggcaggccagtggctcaggcctgtaa
Reference
Zhao, L. H., et al.Genomic and oncogenic preference of HBV integration in hepatocellular carcinoma. Nat Commun ,2016,7: 12992.
Curate