LOC129929564 (ATAC-STARR-seq lymphoblastoid silent region 350) - Rat Genome Database

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Gene: LOC129929564 (ATAC-STARR-seq lymphoblastoid silent region 350) Homo sapiens
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Symbol: LOC129929564
Name: ATAC-STARR-seq lymphoblastoid silent region 350
RGD ID: 329407942
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
GRCh38119,209,936 - 19,210,255 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37119,536,430 - 19,536,749 (+)NCBIGRCh37GRCh37hg19GRCh37
T2T-CHM13v2.0119,033,448 - 19,033,767 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


PMID:35858748  



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Variants in LOC129929564
9 total Variants

1 to 10 of 16 rows
Name
Type
Condition(s)
Position(s)
Clinical significance
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
NM_020765.3(UBR4):c.70G>C (p.Asp24His) single nucleotide variant not specified [RCV004603398] Chr1:19210179 [GRCh38]
Chr1:19536673 [GRCh37]
Chr1:1p36.13		 uncertain significance
NM_020765.3(UBR4):c.47C>T (p.Pro16Leu) single nucleotide variant not specified [RCV004206551] Chr1:19210202 [GRCh38]
Chr1:19536696 [GRCh37]
Chr1:1p36.13		 uncertain significance
NM_020765.3(UBR4):c.76A>G (p.Thr26Ala) single nucleotide variant not specified [RCV004212128] Chr1:19210173 [GRCh38]
Chr1:19536667 [GRCh37]
Chr1:1p36.13		 uncertain significance
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 1p36.13(chr1:19169253-19797307)x3 copy number gain See cases [RCV000141322] Chr1:19169253..19797307 [GRCh38]
Chr1:19495747..20123800 [GRCh37]
Chr1:19368334..19996387 [NCBI36]
Chr1:1p36.13		 likely benign
NM_020765.3(UBR4):c.56C>G (p.Pro19Arg) single nucleotide variant not specified [RCV004282583] Chr1:19210193 [GRCh38]
Chr1:19536687 [GRCh37]
Chr1:1p36.13		 uncertain significance
GRCh38/hg38 1p36.13(chr1:19093306-20063342)x1 copy number loss See cases [RCV000053793] Chr1:19093306..20063342 [GRCh38]
Chr1:19419800..20389835 [GRCh37]
Chr1:19292387..20262422 [NCBI36]
Chr1:1p36.13		 pathogenic
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 1p36.33-35.1(chr1:99125-34026935)x3 copy number gain Trisomy 12p [RCV003447845] Chr1:99125..34026935 [GRCh38]
Chr1:1p36.33-35.1		 pathogenic
1 to 10 of 16 rows

The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD ID
Symbol
Name
LOD
P Value
Trait
Sub Trait
Chr
Start
Stop
Species
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
RefSeq Transcripts NG_162621 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AL357564 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CP068277 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles



Database
Acc Id
Source(s)
COSMIC LOC129929564 COSMIC
GTEx LOC129929564 GTEx
Human Proteome Map LOC129929564 Human Proteome Map
NCBI Gene LOC129929564 ENTREZGENE