LOC112841611 (Sharpr-MPRA regulatory region 7874) - Rat Genome Database

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Gene: LOC112841611 (Sharpr-MPRA regulatory region 7874) Homo sapiens
Analyze
Symbol: LOC112841611
Name: Sharpr-MPRA regulatory region 7874
RGD ID: 38655994
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. The major subregion includes an enhancer that was validated by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in naive human embryonic stem cells, where it is marked by the H3K27ac histone modification. Another subregion was validated as an enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 1:Tss). Another subregion includes an accessible chromatin region used in a lentiviral ReSE (repressive ability of silencer elements) screen that assays for cell survival based on transcriptional repression of an apoptosis-inducing fusion protein. That subregion was identified as a functional silencer in K562 cells. 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
GRCh383101,848,573 - 101,850,192 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh373101,568,049 - 101,568,343 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map3qNCBI
T2T-CHM13v2.03104,561,365 - 104,562,984 (+)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:27701403   PMID:30033119   PMID:32094911   PMID:35858748  


Genomics

Variants

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Variants in LOC112841611
4 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 3q11.1-24(chr3:93800620-145695381)x3 copy number gain See cases [RCV000142340] Chr3:93800620..145695381 [GRCh38]
Chr3:93519464..145413168 [GRCh37]
Chr3:95002154..146895858 [NCBI36]
Chr3:3q11.1-24		 pathogenic
GRCh38/hg38 3q11.1-13.11(chr3:93819623-103888749)x3 copy number gain See cases [RCV000143259] Chr3:93819623..103888749 [GRCh38]
Chr3:93538467..103607593 [GRCh37]
Chr3:95021157..105090283 [NCBI36]
Chr3:3q11.1-13.11		 likely pathogenic|uncertain significance
GRCh38/hg38 3q11.2-13.31(chr3:97795369-115663349)x1 copy number loss See cases [RCV000138186] Chr3:97795369..115663349 [GRCh38]
Chr3:97514213..115382196 [GRCh37]
Chr3:98996903..116864886 [NCBI36]
Chr3:3q11.2-13.31		 pathogenic|uncertain significance
GRCh38/hg38 3q12.3(chr3:101596165-102374145)x3 copy number gain See cases [RCV000134705] Chr3:101596165..102374145 [GRCh38]
Chr3:101315009..102092989 [GRCh37]
Chr3:102797699..103575679 [NCBI36]
Chr3:3q12.3		 likely benign
GRCh38/hg38 3q11.1-21.1(chr3:93886671-123216683)x1 copy number loss See cases [RCV000051543] Chr3:93886671..123216683 [GRCh38]
Chr3:93605515..122935530 [GRCh37]
Chr3:95088205..124418220 [NCBI36]
Chr3:3q11.1-21.1		 pathogenic
NM_031419.4(NFKBIZ):c.40G>C (p.Glu14Gln) single nucleotide variant Inborn genetic diseases [RCV002955317] Chr3:101849668 [GRCh38]
Chr3:101568512 [GRCh37]
Chr3:3q12.3		 uncertain significance
GRCh38/hg38 3q11.1-13.31(chr3:93819623-116887056)x1 copy number loss See cases [RCV000135320] Chr3:93819623..116887056 [GRCh38]
Chr3:93538467..116605903 [GRCh37]
Chr3:95021157..118088593 [NCBI36]
Chr3:3q11.1-13.31		 pathogenic
GRCh38/hg38 3q11.1-21.2(chr3:93979547-124774010)x1 copy number loss Chromosome 3q13.31 deletion syndrome [RCV003327614] Chr3:93979547..124774010 [GRCh38]
Chr3:3q11.1-21.2		 pathogenic
NM_031419.4(NFKBIZ):c.173C>T (p.Ser58Leu) single nucleotide variant Inborn genetic diseases [RCV002728802] Chr3:101849801 [GRCh38]
Chr3:101568645 [GRCh37]
Chr3:3q12.3		 uncertain significance
NM_031419.4(NFKBIZ):c.245T>C (p.Val82Ala) single nucleotide variant Inborn genetic diseases [RCV002704431] Chr3:101849873 [GRCh38]
Chr3:101568717 [GRCh37]
Chr3:3q12.3		 uncertain significance
NM_031419.4(NFKBIZ):c.283C>A (p.Gln95Lys) single nucleotide variant NFKBIZ-related condition [RCV003934110] Chr3:101849911 [GRCh38]
Chr3:101568755 [GRCh37]
Chr3:3q12.3		 likely benign
NM_031419.4(NFKBIZ):c.242C>T (p.Ala81Val) single nucleotide variant NFKBIZ-related condition [RCV003904732] Chr3:101849870 [GRCh38]
Chr3:101568714 [GRCh37]
Chr3:3q12.3		 likely benign
NM_031419.4(NFKBIZ):c.175G>A (p.Ala59Thr) single nucleotide variant Inborn genetic diseases [RCV003291184] Chr3:101849803 [GRCh38]
Chr3:101568647 [GRCh37]
Chr3:3q12.3		 uncertain significance

Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC112841611 COSMIC
GTEx LOC112841611 GTEx
Human Proteome Map LOC112841611 Human Proteome Map
NCBI Gene LOC112841611 ENTREZGENE