LOC125387297 (Sharpr-MPRA regulatory region 3633) - Rat Genome Database

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Gene: LOC125387297 (Sharpr-MPRA regulatory region 3633) Homo sapiens
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Symbol: LOC125387297
Name: Sharpr-MPRA regulatory region 3633
RGD ID: 152975957
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. It 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 K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate 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
GRCh382050,588,132 - 50,588,426 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372049,204,669 - 49,204,963 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map20qNCBI
T2T-CHM13v2.02052,357,790 - 52,358,084 (+)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 20q13.12-13.33(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 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 20q13.13-13.2(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 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 LOC125387297 COSMIC
GTEx LOC125387297 GTEx
Human Proteome Map LOC125387297 Human Proteome Map
NCBI Gene LOC125387297 ENTREZGENE