LOC130056737 (ATAC-STARR-seq lymphoblastoid silent region 6273) - Rat Genome Database

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Gene: LOC130056737 (ATAC-STARR-seq lymphoblastoid silent region 6273) Homo sapiens
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Symbol: LOC130056737
Name: ATAC-STARR-seq lymphoblastoid silent region 6273
RGD ID: 329820239
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
GRCh381534,038,177 - 34,038,236 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371534,330,378 - 34,330,437 (+)NCBIGRCh37GRCh37hg19GRCh37
T2T-CHM13v2.01531,836,364 - 31,836,423 (+)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 15q11.2-14(chr15:23319714-38089582)x1 copy number loss See cases [RCV000135953] Chr15:23319714..38089582 [GRCh38]
Chr15:22698522..38381783 [GRCh37]
Chr15:20249886..36169075 [NCBI36]
Chr15:15q11.2-14		 pathogenic
GRCh38/hg38 15q13.3-14(chr15:32326136-39394068)x1 copy number loss See cases [RCV000051616] Chr15:32326136..39394068 [GRCh38]
Chr15:32618337..39686269 [GRCh37]
Chr15:30405629..37473561 [NCBI36]
Chr15:15q13.3-14		 pathogenic
GRCh38/hg38 15q13.3-14(chr15:32607298-35200429)x3 copy number gain See cases [RCV000051157] Chr15:32607298..35200429 [GRCh38]
Chr15:32899499..35492630 [GRCh37]
Chr15:30686791..33279922 [NCBI36]
Chr15:15q13.3-14		 pathogenic
GRCh38/hg38 15q11.2-14(chr15:25033869-37204304)x1 copy number loss See cases [RCV000143205] Chr15:25033869..37204304 [GRCh38]
Chr15:25279016..37496505 [GRCh37]
Chr15:22830109..35283797 [NCBI36]
Chr15:15q11.2-14		 pathogenic
GRCh38/hg38 15q14(chr15:33813732-34135651)x3 copy number gain See cases [RCV000141146] Chr15:33813732..34135651 [GRCh38]
Chr15:34105933..34427852 [GRCh37]
Chr15:31893225..32215144 [NCBI36]
Chr15:15q14		 uncertain significance
GRCh38/hg38 15q13.3-14(chr15:32640661-34525062) copy number gain Autism spectrum disorder [RCV003883410] Chr15:32640661..34525062 [GRCh38]
Chr15:15q13.3-14		 uncertain significance
GRCh38/hg38 15q11.2-14(chr15:23319714-38545325)x3 copy number gain See cases [RCV000138530] Chr15:23319714..38545325 [GRCh38]
Chr15:22765628..38837526 [GRCh37]
Chr15:20316992..36624818 [NCBI36]
Chr15:15q11.2-14		 pathogenic
GRCh38/hg38 15q13.3-15.1(chr15:32635803-40233825)x1 copy number loss See cases [RCV000051617] Chr15:32635803..40233825 [GRCh38]
Chr15:32928004..40526026 [GRCh37]
Chr15:30715296..38313318 [NCBI36]
Chr15:15q13.3-15.1		 pathogenic

QTLs in Region (GRCh38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2289410BW327_HBody weight QTL 327 (human)3.320.0001Body fat amount151998012945980129Human
1643273BW330_HBody Weight QTL 330 (human)1.050.014Body weightbody mass index152686671952866719Human
2289430BMD7_HBone mineral density QTL 7 (human)3.320.0001Bone mineral density151998012945980129Human
1559411SCL107_HSerum cholesterol level QTL 107 (human)3.88Lipid leveltriglyceride152654355252543552Human
1643523BW284_HBody Weight QTL 284 (human)1.950.0013Body weight152179288947792889Human
2289420BW314_HBody weight QTL 314 (human)2.720.0003Body weightlean mass151998012945980129Human


Expression

RNA-SEQ Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC130056737 COSMIC
GTEx LOC130056737 GTEx
Human Proteome Map LOC130056737 Human Proteome Map
NCBI Gene LOC130056737 ENTREZGENE