LOC129992984 (ATAC-STARR-seq lymphoblastoid silent region 15639) - Rat Genome Database

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Gene: LOC129992984 (ATAC-STARR-seq lymphoblastoid silent region 15639) Homo sapiens
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Symbol: LOC129992984
Name: ATAC-STARR-seq lymphoblastoid silent region 15639
RGD ID: 329813488
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
GRCh384112,515,272 - 112,515,341 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh374113,436,428 - 113,436,497 (+)NCBIGRCh37GRCh37hg19GRCh37
T2T-CHM13v2.04115,823,606 - 115,823,675 (+)NCBIT2T-CHM13v2.0
JBrowse:




Disease Annotations     Click to see Annotation Detail View

References
Additional References at PubMed
PMID:35858748  


Genomics

Variants

.
Variants in LOC129992984
2 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 4q22.3-28.3(chr4:96092893-136410207)x3 copy number gain See cases [RCV000051776] Chr4:96092893..136410207 [GRCh38]
Chr4:97014044..137331362 [GRCh37]
Chr4:97233067..137550812 [NCBI36]
Chr4:4q22.3-28.3		 pathogenic
GRCh38/hg38 4q25-26(chr4:111069785-116691879)x1 copy number loss See cases [RCV000134955] Chr4:111069785..116691879 [GRCh38]
Chr4:111990941..117613035 [GRCh37]
Chr4:112210390..117832483 [NCBI36]
Chr4:4q25-26		 likely pathogenic
NC_000004.10:g.111994000_115504000del3510001 deletion Congenital aniridia [RCV005419942] Chr4:110853395..114363395 [GRCh38]
Chr4:111774551..115284551 [GRCh37]
Chr4:111994000..115504000 [NCBI36]
Chr4:4q25-26		 pathogenic
NC_000004.12:g.110650730_112833790del deletion Axenfeld-Rieger syndrome type 1 [RCV003225703] Chr4:110650730..112833790 [GRCh38]
Chr4:4q25		 likely pathogenic
NM_024019.4(NEUROG2):c.158G>C (p.Arg53Pro) single nucleotide variant not specified [RCV004486845] Chr4:112515318 [GRCh38]
Chr4:113436474 [GRCh37]
Chr4:4q25		 likely benign
NM_024019.4(NEUROG2):c.185G>A (p.Gly62Glu) single nucleotide variant not specified [RCV004832075] Chr4:112515291 [GRCh38]
Chr4:113436447 [GRCh37]
Chr4:4q25		 uncertain significance
NM_024019.4(NEUROG2):c.154C>T (p.Arg52Cys) single nucleotide variant not specified [RCV005381553] Chr4:112515322 [GRCh38]
Chr4:113436478 [GRCh37]
Chr4:4q25		 uncertain significance

QTLs in Region (GRCh38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1643256BW127_HBody Weight QTL 127 (human)1.310.007Body weightbody mass index4106319694132319694Human


Expression

RNA-SEQ Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC129992984 COSMIC
GTEx LOC129992984 GTEx
Human Proteome Map LOC129992984 Human Proteome Map
NCBI Gene LOC129992984 ENTREZGENE