LOC123575643 (Sharpr-MPRA regulatory region 5333) - Rat Genome Database

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Gene: LOC123575643 (Sharpr-MPRA regulatory region 5333) Homo sapiens
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Symbol: LOC123575643
Name: Sharpr-MPRA regulatory region 5333
RGD ID: 150530515
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 the Sharpr-MPRA technique (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 19:H4K20, transcription, primarily H4K20me1, more intronic). [provided by RefSeq, Dec 2021]
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
GRCh3862,189,015 - 2,189,309 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3762,189,249 - 2,189,543 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map6pNCBI
T2T-CHM13v2.062,052,643 - 2,052,937 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


PMID:27701403  



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1 to 10 of 33 rows
Name
Type
Condition(s)
Position(s)
Clinical significance
GRCh38/hg38 6p25.3-25.2(chr6:1796838-2854327)x3 copy number gain See cases [RCV000053338] Chr6:1796838..2854327 [GRCh38]
Chr6:1797072..2854561 [GRCh37]
Chr6:1742071..2799560 [NCBI36]
Chr6:6p25.3-25.2		 uncertain significance
GRCh38/hg38 6p25.3-25.2(chr6:1441186-2351374)x1 copy number loss See cases [RCV000135701] Chr6:1441186..2351374 [GRCh38]
Chr6:1441421..2351608 [GRCh37]
Chr6:1386420..2296607 [NCBI36]
Chr6:6p25.3-25.2		 pathogenic
GRCh38/hg38 6p25.3-25.2(chr6:1943429-2507158)x3 copy number gain See cases [RCV000142065] Chr6:1943429..2507158 [GRCh38]
Chr6:1943663..2507392 [GRCh37]
Chr6:1888662..2452391 [NCBI36]
Chr6:6p25.3-25.2		 likely benign|uncertain significance
GRCh38/hg38 6p25.3-22.3(chr6:155807-17058414)x3 copy number gain See cases [RCV000140307] Chr6:155807..17058414 [GRCh38]
Chr6:155807..17058645 [GRCh37]
Chr6:100807..17166624 [NCBI36]
Chr6:6p25.3-22.3		 pathogenic
GRCh38/hg38 6p25.3-24.3(chr6:163083-9525496)x3 copy number gain See cases [RCV000136567] Chr6:163083..9525496 [GRCh38]
Chr6:163083..9525729 [GRCh37]
Chr6:108083..9633715 [NCBI36]
Chr6:6p25.3-24.3		 pathogenic
GRCh38/hg38 6p25.3-24.3(chr6:156974-7122759)x1 copy number loss See cases [RCV000142299] Chr6:156974..7122759 [GRCh38]
Chr6:156974..7122992 [GRCh37]
Chr6:101974..7067991 [NCBI36]
Chr6:6p25.3-24.3		 pathogenic
GRCh38/hg38 6p25.3-24.2(chr6:156974-11550817)x3 copy number gain See cases [RCV000142295] Chr6:156974..11550817 [GRCh38]
Chr6:156974..11551050 [GRCh37]
Chr6:101974..11659036 [NCBI36]
Chr6:6p25.3-24.2		 likely pathogenic
GRCh38/hg38 6p25.3-25.1(chr6:163083-6062800)x1 copy number loss See cases [RCV000050686] Chr6:163083..6062800 [GRCh38]
Chr6:163083..6063033 [GRCh37]
Chr6:108083..6008032 [NCBI36]
Chr6:6p25.3-25.1		 pathogenic
GRCh38/hg38 6p25.3-25.1(chr6:156974-4946857)x3 copy number gain See cases [RCV000143375] Chr6:156974..4946857 [GRCh38]
Chr6:156974..4947091 [GRCh37]
Chr6:101974..4892090 [NCBI36]
Chr6:6p25.3-25.1		 uncertain significance
GRCh38/hg38 6p25.3-12.3(chr6:156974-46789291)x3 copy number gain See cases [RCV000143497] Chr6:156974..46789291 [GRCh38]
Chr6:156974..46757028 [GRCh37]
Chr6:101974..46864987 [NCBI36]
Chr6:6p25.3-12.3		 pathogenic
1 to 10 of 33 rows

The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD ID
Symbol
Name
LOD
P Value
Trait
Sub Trait
Chr
Start
Stop
Species
2289408BW324_HBody weight QTL 324 (human)3.150.0001Body fat amount6120803913Human
1643418BW282_HBody Weight QTL 282 (human)2.070.001Body weight6119321359Human
2289435BMD4_HBone mineral density QTL 4 (human)3.150.0001Bone mineral density6120803913Human
2292824PRSTS5_HProstate tumor susceptibility QTL 5 (human)Prostate tumor susceptibility6119232373Human
2289320BW390_HBody weight QTL 390 (human)2.13Body weightBMI6119321359Human
1643495BW291_HBody Weight QTL 291 (human)2.13Body weightBMI6119321359Human
RefSeq Transcripts NG_077902 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AL035693 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CP068272 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles



Database
Acc Id
Source(s)
COSMIC LOC123575643 COSMIC
GTEx LOC123575643 GTEx
Human Proteome Map LOC123575643 Human Proteome Map
NCBI Gene LOC123575643 ENTREZGENE