LOC125387291 (Sharpr-MPRA regulatory region 92) - Rat Genome Database

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Gene: LOC125387291 (Sharpr-MPRA regulatory region 92) Homo sapiens
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Symbol: LOC125387291
Name: Sharpr-MPRA regulatory region 92
RGD ID: 152975730
Description: This genomic sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. A subregion was validated as a functional repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). This locus also includes an accessible chromatin subregion 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) 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
GRCh382050,190,732 - 50,191,062 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372048,807,269 - 48,807,599 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map20qNCBI
T2T-CHM13v2.02051,960,235 - 51,960,565 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:27701403   PMID:35858748  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 20q13.13-13.2(chr20:49947237-55875406)x3 copy number gain See cases [RCV000053037] Chr20:49947237..55875406 [GRCh38]
Chr20:48563774..54450462 [GRCh37]
Chr20:47997181..53883869 [NCBI36]
Chr20:20q13.13-13.2		 pathogenic
GRCh38/hg38 20q13.13-13.2(chr20:49731076-51202566)x1 copy number loss See cases [RCV000052767] Chr20:49731076..51202566 [GRCh38]
Chr20:48347613..49819103 [GRCh37]
Chr20:47781020..49252510 [NCBI36]
Chr20:20q13.13-13.2		 pathogenic
GRCh38/hg38 20q13.12-13.33(chr20:44787704-64277321)x3 copy number gain See cases [RCV000053035] Chr20:44787704..64277321 [GRCh38]
Chr20:43416345..62908674 [GRCh37]
Chr20:42849759..62379118 [NCBI36]
Chr20:20q13.12-13.33		 pathogenic
GRCh38/hg38 20p13-q13.33(chr20:99557-64277321)x3 copy number gain See cases [RCV000135859] Chr20:99557..64277321 [GRCh38]
Chr20:80198..62908674 [GRCh37]
Chr20:28198..62379118 [NCBI36]
Chr20:20p13-q13.33		 pathogenic
GRCh38/hg38 20q13.13-13.2(chr20:49989123-51495645)x1 copy number loss See cases [RCV000137268] Chr20:49989123..51495645 [GRCh38]
Chr20:48605660..50112183 [GRCh37]
Chr20:48039067..49545590 [NCBI36]
Chr20:20q13.13-13.2		 likely pathogenic

QTLs in Region (GRCh38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2292864PRSTS43_HProstate tumor susceptibility QTL 43 (human)0.620.05Prostate tumor susceptibility204730303964444167Human
1300007BP29_HBlood pressure QTL 29 (human)Blood pressurehypertension susceptibility203653600562536005Human


Expression

RNA-SEQ Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC125387291 COSMIC
GTEx LOC125387291 GTEx
Human Proteome Map LOC125387291 Human Proteome Map
NCBI Gene LOC125387291 ENTREZGENE