LOC129929532 (ATAC-STARR-seq lymphoblastoid silent region 334) - Rat Genome Database

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Gene: LOC129929532 (ATAC-STARR-seq lymphoblastoid silent region 334) Homo sapiens
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Symbol: LOC129929532
Name: ATAC-STARR-seq lymphoblastoid silent region 334
RGD ID: 329410831
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
GRCh38116,625,022 - 16,625,091 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37116,951,517 - 16,951,586 (+)NCBIGRCh37GRCh37hg19GRCh37
T2T-CHM13v2.0116,252,503 - 16,252,572 (+)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 1p36.13(chr1:16621632-16905322)x1 copy number loss See cases [RCV000135910] Chr1:16621632..16905322 [GRCh38]
Chr1:16948127..17231817 [GRCh37]
Chr1:16820714..17104404 [NCBI36]
Chr1:1p36.13		 benign
GRCh38/hg38 1p36.21-36.13(chr1:13619979-18466172)x3 copy number gain See cases [RCV000051799] Chr1:13619979..18466172 [GRCh38]
Chr1:13946474..18792666 [GRCh37]
Chr1:13819061..18665253 [NCBI36]
Chr1:1p36.21-36.13		 pathogenic
GRCh38/hg38 1p36.21-36.12(chr1:15385267-20980349)x1 copy number loss See cases [RCV000051146] Chr1:15385267..20980349 [GRCh38]
Chr1:15711763..21306842 [GRCh37]
Chr1:15584350..21179429 [NCBI36]
Chr1:1p36.21-36.12		 pathogenic
GRCh38/hg38 1p36.13(chr1:16615158-16905322)x3 copy number gain See cases [RCV000135921] Chr1:16615158..16905322 [GRCh38]
Chr1:16941653..17231817 [GRCh37]
Chr1:16814240..17104404 [NCBI36]
Chr1:1p36.13		 benign
GRCh38/hg38 1p36.13(chr1:16600282-16722267)x1 copy number loss See cases [RCV000136213] Chr1:16600282..16722267 [GRCh38]
Chr1:16926777..17048762 [GRCh37]
Chr1:16799364..16921349 [NCBI36]
Chr1:1p36.13		 benign
GRCh38/hg38 1p36.13(chr1:16600450-16761944)x3 copy number gain See cases [RCV000139053] Chr1:16600450..16761944 [GRCh38]
Chr1:16926945..17088439 [GRCh37]
Chr1:16799532..16961026 [NCBI36]
Chr1:1p36.13		 likely benign
GRCh38/hg38 1p36.13(chr1:16487877-16778041)x3 copy number gain See cases [RCV000136781] Chr1:16487877..16778041 [GRCh38]
Chr1:16814372..17104536 [GRCh37]
Chr1:16686959..16977123 [NCBI36]
Chr1:1p36.13		 benign
GRCh38/hg38 1p36.13(chr1:16600450-16856300)x3 copy number gain See cases [RCV000139689] Chr1:16600450..16856300 [GRCh38]
Chr1:16926945..17182795 [GRCh37]
Chr1:16799532..17055382 [NCBI36]
Chr1:1p36.13		 likely benign
GRCh38/hg38 1p36.13(chr1:16487877-16778041)x1 copy number loss See cases [RCV000136782] Chr1:16487877..16778041 [GRCh38]
Chr1:16814372..17104536 [GRCh37]
Chr1:16686959..16977123 [NCBI36]
Chr1:1p36.13		 benign
GRCh38/hg38 1p36.21-36.13(chr1:15681812-19662339)x1 copy number loss See cases [RCV000138070] Chr1:15681812..19662339 [GRCh38]
Chr1:16008307..19988832 [GRCh37]
Chr1:15880894..19861419 [NCBI36]
Chr1:1p36.21-36.13		 pathogenic
GRCh38/hg38 1p36.31-36.13(chr1:5363826-18360302)x1 copy number loss See cases [RCV000142771] Chr1:5363826..18360302 [GRCh38]
Chr1:5423886..18686796 [GRCh37]
Chr1:5323746..18559383 [NCBI36]
Chr1:1p36.31-36.13		 pathogenic
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
GRCh38/hg38 1p36.32-36.13(chr1:3006193-17688934)x1 copy number loss See cases [RCV000053714] Chr1:3006193..17688934 [GRCh38]
Chr1:2922757..18015429 [GRCh37]
Chr1:2912617..17888016 [NCBI36]
Chr1:1p36.32-36.13		 pathogenic

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
1298463BP9_HBlood pressure QTL 9 (human)3.9Blood pressurehypertension susceptibility1125188105Human
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


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC129929532 COSMIC
GTEx LOC129929532 GTEx
Human Proteome Map LOC129929532 Human Proteome Map
NCBI Gene LOC129929532 ENTREZGENE