LOC116286196 (CRISPRi-validated cis-regulatory element chr19.6204) - Rat Genome Database

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Gene: LOC116286196 (CRISPRi-validated cis-regulatory element chr19.6204) Homo sapiens
Analyze
Symbol: LOC116286196
Name: CRISPRi-validated cis-regulatory element chr19.6204
RGD ID: 38670302
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. A subregion was validated as a cis-regulatory element for the UBE2S (ubiquitin conjugating enzyme E2 S) gene on chromosome 19 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. Another subregion was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay in naive human embryonic stem cells, where it is marked by the H3K4me1 histone modification. [provided by RefSeq, Jan 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
GRCh381955,371,979 - 55,373,156 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371955,883,527 - 55,884,524 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map19qNCBI
T2T-CHM13v2.01958,467,466 - 58,468,643 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:22955616   PMID:22955617   PMID:30033119   PMID:30612741  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 19q13.33-13.43(chr19:49907832-58557889)x3 copy number gain See cases [RCV000052925] Chr19:49907832..58557889 [GRCh38]
Chr19:50411089..59069256 [GRCh37]
Chr19:55102901..63761068 [NCBI36]
Chr19:19q13.33-13.43		 pathogenic
GRCh38/hg38 19q13.41-13.43(chr19:51141518-58539965)x3 copy number gain See cases [RCV000052926] Chr19:51141518..58539965 [GRCh38]
Chr19:51644775..59051332 [GRCh37]
Chr19:56336587..63743144 [NCBI36]
Chr19:19q13.41-13.43		 pathogenic
GRCh38/hg38 19q13.41-13.43(chr19:52143873-58445521)x3 copy number gain See cases [RCV000142008] Chr19:52143873..58445521 [GRCh38]
Chr19:52647126..58956888 [GRCh37]
Chr19:57338938..63648700 [NCBI36]
Chr19:19q13.41-13.43		 pathogenic
GRCh38/hg38 19q13.42(chr19:55066790-55789870)x3 copy number gain See cases [RCV000142067] Chr19:55066790..55789870 [GRCh38]
Chr19:55578158..56301236 [GRCh37]
Chr19:60269970..60993048 [NCBI36]
Chr19:19q13.42		 uncertain significance
GRCh38/hg38 19q13.42-13.43(chr19:55037146-56982033)x3 copy number gain See cases [RCV000142245] Chr19:55037146..56982033 [GRCh38]
Chr19:55548514..57493401 [GRCh37]
Chr19:60240326..62185213 [NCBI36]
Chr19:19q13.42-13.43		 uncertain significance
GRCh38/hg38 19q13.41-13.43(chr19:52612432-58581203)x3 copy number gain See cases [RCV000134174] Chr19:52612432..58581203 [GRCh38]
Chr19:53115685..59092570 [GRCh37]
Chr19:57807497..63784382 [NCBI36]
Chr19:19q13.41-13.43		 pathogenic
GRCh38/hg38 19q13.41-13.43(chr19:52955056-58581203)x3 copy number gain See cases [RCV000134139] Chr19:52955056..58581203 [GRCh38]
Chr19:53458309..59092570 [GRCh37]
Chr19:58150121..63784382 [NCBI36]
Chr19:19q13.41-13.43		 pathogenic
GRCh38/hg38 19q13.33-13.43(chr19:50152520-58581203)x3 copy number gain See cases [RCV000135843] Chr19:50152520..58581203 [GRCh38]
Chr19:50655777..59092570 [GRCh37]
Chr19:55347589..63784382 [NCBI36]
Chr19:19q13.33-13.43		 pathogenic
GRCh38/hg38 19q13.42-13.43(chr19:55048514-56972458)x3 copy number gain See cases [RCV000138139] Chr19:55048514..56972458 [GRCh38]
Chr19:55595687..57483826 [GRCh37]
Chr19:60251694..62175638 [NCBI36]
Chr19:19q13.42-13.43		 likely pathogenic
GRCh38/hg38 19q13.33-13.43(chr19:47908540-58539965)x3 copy number gain See cases [RCV000052914] Chr19:47908540..58539965 [GRCh38]
Chr19:48411797..59051332 [GRCh37]
Chr19:53103609..63743144 [NCBI36]
Chr19:19q13.33-13.43		 pathogenic
GRCh38/hg38 19q13.33-13.43(chr19:47929575-58572206)x3 copy number gain See cases [RCV000052915] Chr19:47929575..58572206 [GRCh38]
Chr19:48432832..59083573 [GRCh37]
Chr19:53124644..63775385 [NCBI36]
Chr19:19q13.33-13.43		 pathogenic
GRCh38/hg38 19q13.33-13.43(chr19:50191219-58535818)x3 copy number gain See cases [RCV000050883] Chr19:50191219..58535818 [GRCh38]
Chr19:50694476..59047185 [GRCh37]
Chr19:55386288..63738997 [NCBI36]
Chr19:19q13.33-13.43		 pathogenic

Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC116286196 COSMIC
GTEx LOC116286196 GTEx
Human Proteome Map LOC116286196 Human Proteome Map
NCBI Gene LOC116286196 ENTREZGENE