LOC116268460 (CRISPRi-validated cis-regulatory element chr14.1904) - Rat Genome Database

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Gene: LOC116268460 (CRISPRi-validated cis-regulatory element chr14.1904) Homo sapiens
Analyze
Symbol: LOC116268460
Name: CRISPRi-validated cis-regulatory element chr14.1904
RGD ID: 38668102
Description: This genomic region represents a DNase I hypersensitive site (DHS) that was predicted to be an enhancer by the ENCODE (ENCyclopedia Of DNA Elements) project based on various combinations of H3K27 acetylation and binding of p300, GATA1 and RNA polymerase II in K562 erythroleukemia cells. It was validated as a high-confidence cis-regulatory element for the GPR68 (G protein-coupled receptor 68) gene on chromosome 14 based on multiplex CRISPR/Cas9-mediated perturbation 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) 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
GRCh381491,264,382 - 91,265,017 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371491,730,726 - 91,731,361 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map14qNCBI
T2T-CHM13v2.01485,489,869 - 85,490,505 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:22955616   PMID:22955617   PMID:30612741   PMID:35858748  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 14q11.2-32.33(chr14:20043514-106877229)x3 copy number gain See cases [RCV000143373] Chr14:20043514..106877229 [GRCh38]
Chr14:20511673..107285437 [GRCh37]
Chr14:19581513..106356482 [NCBI36]
Chr14:14q11.2-32.33		 pathogenic
GRCh38/hg38 14q24.3-32.33(chr14:77222795-106879298)x3 copy number gain See cases [RCV000138230] Chr14:77222795..106879298 [GRCh38]
Chr14:77689138..107287505 [GRCh37]
Chr14:76758891..106358550 [NCBI36]
Chr14:14q24.3-32.33		 pathogenic
GRCh38/hg38 14q24.3-32.33(chr14:73655772-106879298)x3 copy number gain See cases [RCV000134000] Chr14:73655772..106879298 [GRCh38]
Chr14:74122475..107287505 [GRCh37]
Chr14:73192228..106358550 [NCBI36]
Chr14:14q24.3-32.33		 pathogenic
GRCh38/hg38 14q31.3-32.33(chr14:86094030-106832642)x3 copy number gain See cases [RCV000052295] Chr14:86094030..106832642 [GRCh38]
Chr14:86560374..107240869 [GRCh37]
Chr14:85630127..106311914 [NCBI36]
Chr14:14q31.3-32.33		 pathogenic
GRCh38/hg38 14q32.11(chr14:90495001-91296461)x3 copy number gain See cases [RCV000052086] Chr14:90495001..91296461 [GRCh38]
Chr14:90961345..91762805 [GRCh37]
Chr14:90031098..90832558 [NCBI36]
Chr14:14q32.11		 uncertain significance
GRCh38/hg38 14q32.11-32.13(chr14:90255156-95274696)x1 copy number loss See cases [RCV000051551] Chr14:90255156..95274696 [GRCh38]
Chr14:90721500..95741033 [GRCh37]
Chr14:89791253..94810786 [NCBI36]
Chr14:14q32.11-32.13		 pathogenic
GRCh38/hg38 14q31.2-32.33(chr14:83912345-106855405)x3 copy number gain See cases [RCV000052294] Chr14:83912345..106855405 [GRCh38]
Chr14:84378689..107263620 [GRCh37]
Chr14:83448442..106334665 [NCBI36]
Chr14:14q31.2-32.33		 pathogenic
GRCh38/hg38 14q11.2-32.33(chr14:20151149-106855263)x3 copy number gain See cases [RCV000135543] Chr14:20151149..106855263 [GRCh38]
Chr14:20619308..107263478 [GRCh37]
Chr14:19689148..106334523 [NCBI36]
Chr14:14q11.2-32.33		 pathogenic

Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC116268460 COSMIC
GTEx LOC116268460 GTEx
Human Proteome Map LOC116268460 Human Proteome Map
NCBI Gene LOC116268460 ENTREZGENE