LOC129935043 (ATAC-STARR-seq lymphoblastoid silent region 12066) - Rat Genome Database

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Gene: LOC129935043 (ATAC-STARR-seq lymphoblastoid silent region 12066) Homo sapiens
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Symbol: LOC129935043
Name: ATAC-STARR-seq lymphoblastoid silent region 12066
RGD ID: 329409757
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
GRCh382165,193,304 - 165,193,353 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372166,049,814 - 166,049,863 (+)NCBIGRCh37GRCh37hg19GRCh37
T2T-CHM13v2.02165,650,636 - 165,650,685 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:35858748  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 2q24.3(chr2:165155128-166062451)x1 copy number loss Epilepsy of infancy with migrating focal seizures [RCV002286319] Chr2:165155128..166062451 [GRCh38]
Chr2:2q24.3		 pathogenic
GRCh38/hg38 2q24.3(chr2:164920562-167536439)x3 copy number gain See cases [RCV000133953] Chr2:164920562..167536439 [GRCh38]
Chr2:165777072..168392949 [GRCh37]
Chr2:165485318..168101195 [NCBI36]
Chr2:2q24.3		 pathogenic
GRCh38/hg38 2q24.3-31.1(chr2:164850117-175559190)x1 copy number loss See cases [RCV000051201] Chr2:164850117..175559190 [GRCh38]
Chr2:165706627..176423918 [GRCh37]
Chr2:165414873..176132164 [NCBI36]
Chr2:2q24.3-31.1		 pathogenic
NC_000002.11:g.(?_165946660)_(166246334_?)dup duplication Seizures, benign familial infantile, 3 [RCV000708501]|not provided [RCV003106026] Chr2:165090150..165389824 [GRCh38]
Chr2:165946660..166246334 [GRCh37]
Chr2:2q24.3		 uncertain significance|no classifications from unflagged records
GRCh38/hg38 2q24.1-31.1(chr2:154294042-175989372)x3 copy number gain See cases [RCV000142286] Chr2:154294042..175989372 [GRCh38]
Chr2:155150555..176854100 [GRCh37]
Chr2:154858801..176562346 [NCBI36]
Chr2:2q24.1-31.1		 pathogenic
GRCh38/hg38 2q24.3(chr2:164941760-165764726)x3 copy number gain See cases [RCV000142015] Chr2:164941760..165764726 [GRCh38]
Chr2:165798270..166621236 [GRCh37]
Chr2:165506516..166329482 [NCBI36]
Chr2:2q24.3		 likely pathogenic
NC_000002.12:g.(?_165090130)_(166286643_?)del deletion Early infantile epileptic encephalopathy with suppression bursts [RCV000808624]|Neuropathy, hereditary sensory and autonomic, type 2A [RCV001387894] Chr2:165090130..166286643 [GRCh38]
Chr2:165946640..167143153 [GRCh37]
Chr2:2q24.3		 pathogenic
GRCh38/hg38 2q24.1-24.3(chr2:154366788-167048902)x3 copy number gain See cases [RCV000052950] Chr2:154366788..167048902 [GRCh38]
Chr2:155223300..167905412 [GRCh37]
Chr2:154931546..167613658 [NCBI36]
Chr2:2q24.1-24.3		 pathogenic
NC_000002.12:g.(?_165090130)_(166228992_?)del deletion Early infantile epileptic encephalopathy with suppression bursts [RCV000636624]|Neuropathy, hereditary sensory and autonomic, type 2A [RCV001387895] Chr2:165090130..166228992 [GRCh38]
Chr2:165946640..167085502 [GRCh37]
Chr2:2q24.3		 pathogenic
NC_000002.11:g.(?_165946640)_(166246354_?)dup duplication Seizures, benign familial infantile, 3 [RCV000640656] Chr2:165090130..165389844 [GRCh38]
Chr2:165946640..166246354 [GRCh37]
Chr2:2q24.3		 uncertain significance
GRCh38/hg38 2q24.3-32.1(chr2:163965382-182195062)x1 copy number loss See cases [RCV000054122] Chr2:163965382..182195062 [GRCh38]
Chr2:164821892..183059789 [GRCh37]
Chr2:164530138..182768034 [NCBI36]
Chr2:2q24.3-32.1		 pathogenic
GRCh38/hg38 2q24.3(chr2:163455290-166962322)x1 copy number loss See cases [RCV000054119] Chr2:163455290..166962322 [GRCh38]
Chr2:164311800..167818832 [GRCh37]
Chr2:164020046..167527078 [NCBI36]
Chr2:2q24.3		 pathogenic
GRCh38/hg38 2q24.3-31.1(chr2:164066038-172097886)x1 copy number loss See cases [RCV000054123] Chr2:164066038..172097886 [GRCh38]
Chr2:164922548..172962614 [GRCh37]
Chr2:164630794..172670860 [NCBI36]
Chr2:2q24.3-31.1		 pathogenic
GRCh38/hg38 2q24.3(chr2:163419387-165682938)x1 copy number loss See cases [RCV000137581] Chr2:163419387..165682938 [GRCh38]
Chr2:164275897..166539448 [GRCh37]
Chr2:163984143..166247694 [NCBI36]
Chr2:2q24.3		 pathogenic|likely pathogenic
GRCh38/hg38 2q24.1-24.3(chr2:158382388-166605758)x1 copy number loss See cases [RCV000051003] Chr2:158382388..166605758 [GRCh38]
Chr2:159238900..167462268 [GRCh37]
Chr2:158947146..167170514 [NCBI36]
Chr2:2q24.1-24.3		 pathogenic
NC_000002.12:g.(?_165090130)_(166311776_?)del deletion Early infantile epileptic encephalopathy with suppression bursts [RCV000807258]|Neuropathy, hereditary sensory and autonomic, type 2A [RCV003117597]|Seizures, benign familial infantile, 3 [RCV003106069]|not provided [RCV003106068] Chr2:165090130..166311776 [GRCh38]
Chr2:165946640..167168286 [GRCh37]
Chr2:2q24.3		 pathogenic|uncertain significance|no classifications from unflagged records

Expression

RNA-SEQ Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC129935043 COSMIC
GTEx LOC129935043 GTEx
Human Proteome Map LOC129935043 Human Proteome Map
NCBI Gene LOC129935043 ENTREZGENE