LINC02596 (long intergenic non-protein coding RNA 2596) - Rat Genome Database

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Gene: LINC02596 (long intergenic non-protein coding RNA 2596) Homo sapiens
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Symbol: LINC02596
Name: long intergenic non-protein coding RNA 2596
RGD ID: 13708585
HGNC Page HGNC:53948
Description:
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38121,586,448 - 21,591,187 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl121,586,472 - 21,591,198 (+)EnsemblGRCh38hg38GRCh38
GRCh37121,912,941 - 21,917,680 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map1p36.12NCBI
CHM1_1122,024,193 - 22,029,688 (+)NCBICHM1_1
T2T-CHM13v2.0121,410,360 - 21,415,099 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:29568943  


Genomics

Variants

.
Variants in LINC02596
2 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 1p36.12(chr1:21399130-22696747)x1 copy number loss See cases [RCV000138071] Chr1:21399130..22696747 [GRCh38]
Chr1:21725623..23023240 [GRCh37]
Chr1:21598210..22895827 [NCBI36]
Chr1:1p36.12		 likely pathogenic|uncertain significance
GRCh38/hg38 1p36.13-36.12(chr1:18347821-22512894)x1 copy number loss See cases [RCV000053789] Chr1:18347821..22512894 [GRCh38]
Chr1:18674315..22839387 [GRCh37]
Chr1:18546902..22711974 [NCBI36]
Chr1:1p36.13-36.12		 pathogenic
GRCh38/hg38 1p36.22-36.12(chr1:10556797-22557907)x1 copy number loss See cases [RCV000053760] Chr1:10556797..22557907 [GRCh38]
Chr1:10616854..22884400 [GRCh37]
Chr1:10539441..22756987 [NCBI36]
Chr1:1p36.22-36.12		 pathogenic
GRCh38/hg38 1p36.12(chr1:21495674-22049209)x3 copy number gain See cases [RCV000137363] Chr1:21495674..22049209 [GRCh38]
Chr1:21822167..22375702 [GRCh37]
Chr1:21694754..22248289 [NCBI36]
Chr1:1p36.12		 uncertain significance
GRCh38/hg38 1p36.33-35.1(chr1:99125-34026935)x3 copy number gain Trisomy 12p [RCV003447845] Chr1:99125..34026935 [GRCh38]
Chr1:1p36.33-35.1		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:385
Count of miRNA genes:340
Interacting mature miRNAs:370
Transcripts:ENST00000457706
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCh38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1298451OSTEAR17_HOsteoarthritis QTL 17 (human)2.40.0004Joint/bone inflammationosteoarthritis11125188105Human
1576329MYI9_HMyocardial infarction susceptibility QTL 9 (human)12Myocardial infarction susceptibilityearly-onset1758550333585503Human
407165024GWAS814000_Halkaline phosphatase measurement QTL GWAS814000 (human)2e-152alkaline phosphatase measurementblood alkaline phosphatase activity level (CMO:0000576)12159074121590742Human
1298463BP9_HBlood pressure QTL 9 (human)3.9Blood pressurehypertension susceptibility1125188105Human
407173048GWAS822024_Halkaline phosphatase measurement QTL GWAS822024 (human)6e-11alkaline phosphatase measurementblood alkaline phosphatase activity level (CMO:0000576)12159034421590345Human
1576325MYI1_HMyocardial infarction susceptibility QTL 1 (human)11.681e-12Myocardial infarction susceptibilityearly-onset1758550333585503Human
1643380BW316_HBody weight QTL 316 (human)2.620.0002Body weightBMI1758550333585503Human


Expression

RNA-SEQ Expression

adipose tissue
alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
entire extraembryonic component
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
477 575 569 493 1766 1207 1333 1 164 1100 136 568 2531 2419 22 1404 335 784 1129 31

Sequence


Ensembl Acc Id: ENST00000457706
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl121,586,472 - 21,591,198 (+)Ensembl
Ensembl Acc Id: ENST00000844409
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl121,587,046 - 21,591,188 (+)Ensembl
RefSeq Acc Id: NR_187321
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38121,586,448 - 21,591,187 (+)NCBI
T2T-CHM13v2.0121,410,360 - 21,415,099 (+)NCBI

Additional Information

Database Acc Id Source(s)
COSMIC LINC02596 COSMIC
Ensembl Genes ENSG00000233431 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000457706 ENTREZGENE
GTEx ENSG00000233431 GTEx
HGNC ID HGNC:53948 ENTREZGENE
Human Proteome Map LINC02596 Human Proteome Map
NCBI Gene LINC02596 ENTREZGENE
RNAcentral URS00026A2756 RNACentral