LOC129994533 (ATAC-STARR-seq lymphoblastoid silent region 16302) - Rat Genome Database

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Gene: LOC129994533 (ATAC-STARR-seq lymphoblastoid silent region 16302) Homo sapiens
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Symbol: LOC129994533
Name: ATAC-STARR-seq lymphoblastoid silent region 16302
RGD ID: 329833152
Description: This genomic sequence represents an accessible chromatin region that was validated as a silencer based on its ability to repress an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
Type: biological-region
RefSeq Status: REVIEWED
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385131,165,376 - 131,165,425 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh375130,501,069 - 130,501,118 (+)NCBIGRCh37GRCh37hg19GRCh37
T2T-CHM13v2.05131,684,367 - 131,684,416 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:35858748  


Genomics

Variants

.
Variants in LOC129994533
3 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NC_000005.10:g.131165401C>T single nucleotide variant not provided [RCV001571240] Chr5:131165401 [GRCh38]
Chr5:130501094 [GRCh37]
Chr5:5q23.3		 likely benign
GRCh38/hg38 5q23.3-33.2(chr5:130860928-155321811)x3 copy number gain See cases [RCV000051193] Chr5:130860928..155321811 [GRCh38]
Chr5:130196621..154701371 [GRCh37]
Chr5:130224520..154681564 [NCBI36]
Chr5:5q23.3-33.2		 pathogenic
GRCh38/hg38 5q23.3-33.2(chr5:129847794-153353546)x3 copy number gain See cases [RCV000138808] Chr5:129847794..153353546 [GRCh38]
Chr5:129183487..152733106 [GRCh37]
Chr5:129211386..152713299 [NCBI36]
Chr5:5q23.3-33.2		 pathogenic
GRCh38/hg38 5q23.2-31.1(chr5:126438406-132873967)x1 copy number loss See cases [RCV000052109] Chr5:126438406..132873967 [GRCh38]
Chr5:125774098..132209659 [GRCh37]
Chr5:125801997..132237558 [NCBI36]
Chr5:5q23.2-31.1		 pathogenic
GRCh38/hg38 5q14.3-31.1(chr5:91411708-131319563)x1 copy number loss See cases [RCV000143746] Chr5:91411708..131319563 [GRCh38]
Chr5:90707525..130655256 [GRCh37]
Chr5:90743281..130683155 [NCBI36]
Chr5:5q14.3-31.1		 pathogenic
GRCh38/hg38 5q23.3(chr5:130803575-131187009)x1 copy number loss See cases [RCV000141926] Chr5:130803575..131187009 [GRCh38]
Chr5:130139268..130522702 [GRCh37]
Chr5:130167167..130550601 [NCBI36]
Chr5:5q23.3		 likely benign|uncertain significance
NM_005340.6(HINT1):c.-176A>G single nucleotide variant not provided [RCV000841654] Chr5:131165381 [GRCh38]
Chr5:130501074 [GRCh37]
Chr5:5q23.3		 benign
GRCh38/hg38 5q21.3-33.2(chr5:106619588-156124387)x1 copy number loss See cases [RCV000053524] Chr5:106619588..156124387 [GRCh38]
Chr5:105955289..155551397 [GRCh37]
Chr5:105983188..155483975 [NCBI36]
Chr5:5q21.3-33.2		 pathogenic
NC_000005.10:g.131165380C>T single nucleotide variant not provided [RCV001544915] Chr5:131165380 [GRCh38]
Chr5:130501073 [GRCh37]
Chr5:5q23.3		 likely benign
GRCh38/hg38 5q23.1-31.1(chr5:116677122-132686163)x1 copy number loss See cases [RCV000053525] Chr5:116677122..132686163 [GRCh38]
Chr5:116012818..132021855 [GRCh37]
Chr5:116040717..132049754 [NCBI36]
Chr5:5q23.1-31.1		 pathogenic

Expression

RNA-SEQ Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC129994533 COSMIC
GTEx LOC129994533 GTEx
Human Proteome Map LOC129994533 Human Proteome Map
NCBI Gene LOC129994533 ENTREZGENE