LOC130056932 (ATAC-STARR-seq lymphoblastoid silent region 6377) - Rat Genome Database

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Gene: LOC130056932 (ATAC-STARR-seq lymphoblastoid silent region 6377) Homo sapiens
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Symbol: LOC130056932
Name: ATAC-STARR-seq lymphoblastoid silent region 6377
RGD ID: 329826697
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
GRCh381542,736,735 - 42,736,874 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371543,028,933 - 43,029,072 (+)NCBIGRCh37GRCh37hg19GRCh37
T2T-CHM13v2.01540,543,867 - 40,544,006 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References
Additional References at PubMed
PMID:35858748  


Genomics

Variants

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Variants in LOC130056932
3 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_138477.4(CDAN1):c.91-88C>T single nucleotide variant not provided [RCV001684923] Chr15:42736868 [GRCh38]
Chr15:43029066 [GRCh37]
Chr15:15q15.2		 benign
NM_138477.4(CDAN1):c.114G>A (p.Ala38=) single nucleotide variant Anemia, congenital dyserythropoietic, type 1a [RCV003763046]|not provided [RCV002169150] Chr15:42736757 [GRCh38]
Chr15:43028955 [GRCh37]
Chr15:15q15.2		 likely benign
GRCh38/hg38 15q15.2-15.3(chr15:42566761-43847106)x1 copy number loss See cases [RCV000137921] Chr15:42566761..43847106 [GRCh38]
Chr15:42858959..44139304 [GRCh37]
Chr15:40646251..41926596 [NCBI36]
Chr15:15q15.2-15.3		 likely pathogenic
NM_138477.4(CDAN1):c.134T>C (p.Leu45Pro) single nucleotide variant Anemia, congenital dyserythropoietic, type 1a [RCV003388739] Chr15:42736737 [GRCh38]
Chr15:43028935 [GRCh37]
Chr15:15q15.2		 uncertain significance

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
2299958PRSTS330_HProstate tumor susceptibility QTL 330 (human)1.020.0151Prostate tumor susceptibility153479023060790230Human
1643523BW284_HBody Weight QTL 284 (human)1.950.0013Body weight152179288947792889Human
1559354LDLPS4_HLow density lipoprotein particle size QTL 4 (human)2.20.019LDL particle size153479023060790230Human
2289420BW314_HBody weight QTL 314 (human)2.720.0003Body weightlean mass151998012945980129Human


Expression

RNA-SEQ Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC130056932 COSMIC
GTEx LOC130056932 GTEx
Human Proteome Map LOC130056932 Human Proteome Map
NCBI Gene LOC130056932 ENTREZGENE