LOC117125597 (CRISPRi-FlowFISH-validated CALR, DNASE2 and KLF1 regulatory element) - Rat Genome Database
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Gene: LOC117125597 (CRISPRi-FlowFISH-validated CALR, DNASE2 and KLF1 regulatory element) Homo sapiens
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Symbol: LOC117125597
Name: CRISPRi-FlowFISH-validated CALR, DNASE2 and KLF1 regulatory element
RGD ID: 38661899
Description: This genomic region was predicted to be an enhancer based on an activity-by-contact (ABC) model that predicts enhancer-gene connections, where the putative enhancer strength is measured by DNase I hypersensitivity and H3K27 acetylation, and the contact frequency by Hi-C. It was validated as a negatively-acting cis-regulatory element for each of the CALR (calreticulin), DNASE2 (deoxyribonuclease 2, lysosomal) and KLF1 (Kruppel like factor 1) genes based on CRISPR/Cas9-mediated perturbation (CRISPRi-FlowFISH method) in K562 erythroleukemia cells. [provided by RefSeq, Mar 2020]
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
GRCh381913,102,611 - 13,103,531 (+)NCBIGRCh38GRCh38hg38GRCh38
Cytogenetic Map19pNCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:31784727  


Genomics


Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts NG_068135 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC005546 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 19p13.13(chr19:12850595-13290954)x3 copy number gain See cases [RCV000052911] Chr19:12850595..13290954 [GRCh38]
Chr19:12961409..13401768 [GRCh37]
Chr19:12822409..13262768 [NCBI36]
Chr19:19p13.13
pathogenic
GRCh38/hg38 19p13.2-13.13(chr19:8831147-13331227)x3 copy number gain See cases [RCV000052908] Chr19:8831147..13331227 [GRCh38]
Chr19:8941823..13442041 [GRCh37]
Chr19:8802823..13303041 [NCBI36]
Chr19:19p13.2-13.13
likely pathogenic
GRCh38/hg38 19p13.13(chr19:12974394-13408586)x1 copy number loss See cases [RCV000138197] Chr19:12974394..13408586 [GRCh38]
Chr19:13085208..13519400 [GRCh37]
Chr19:12946208..13380400 [NCBI36]
Chr19:19p13.13
pathogenic
GRCh38/hg38 19p13.13(chr19:12813597-13119698)x3 copy number gain See cases [RCV000054144] Chr19:12813597..13119698 [GRCh38]
Chr19:12924411..13230512 [GRCh37]
Chr19:12785411..13091512 [NCBI36]
Chr19:19p13.13
uncertain significance
GRCh38/hg38 19p13.13(chr19:12978943-13236134)x3 copy number gain See cases [RCV000136559] Chr19:12978943..13236134 [GRCh38]
Chr19:13089757..13346948 [GRCh37]
Chr19:12950757..13207948 [NCBI36]
Chr19:19p13.13
likely pathogenic|uncertain significance
GRCh38/hg38 19p13.2-13.13(chr19:11517825-13225287)x1 copy number loss See cases [RCV000053945] Chr19:11517825..13225287 [GRCh38]
Chr19:11628640..13336101 [GRCh37]
Chr19:11489640..13197101 [NCBI36]
Chr19:19p13.2-13.13
pathogenic
GRCh38/hg38 19p13.2-q13.31(chr19:11227942-44626354)x3 copy number gain See cases [RCV000133888] Chr19:11227942..44626354 [GRCh38]
Chr19:11338618..45129651 [GRCh37]
Chr19:11199618..49821491 [NCBI36]
Chr19:19p13.2-q13.31
pathogenic
GRCh38/hg38 19p13.13(chr19:13034666-13283686)x1 copy number loss See cases [RCV000135352] Chr19:13034666..13283686 [GRCh38]
Chr19:13145480..13394500 [GRCh37]
Chr19:13006480..13255500 [NCBI36]
Chr19:19p13.13
pathogenic
GRCh38/hg38 19p13.2-13.13(chr19:10319474-13777860)x1 copy number loss See cases [RCV000141568] Chr19:10319474..13777860 [GRCh38]
Chr19:10430150..13888674 [GRCh37]
Chr19:10291150..13749674 [NCBI36]
Chr19:19p13.2-13.13
pathogenic
GRCh38/hg38 19p13.2-13.12(chr19:12580427-14742673)x1 copy number loss See cases [RCV000135937] Chr19:12580427..14742673 [GRCh38]
Chr19:12691241..14853485 [GRCh37]
Chr19:12552241..14714485 [NCBI36]
Chr19:19p13.2-13.12
pathogenic|likely pathogenic
GRCh38/hg38 19p13.2-13.12(chr19:11525163-14155021)x1 copy number loss See cases [RCV000136909] Chr19:11525163..14155021 [GRCh38]
Chr19:11635978..14265833 [GRCh37]
Chr19:11496978..14126833 [NCBI36]
Chr19:19p13.2-13.12
pathogenic
GRCh38/hg38 19p13.2-13.12(chr19:10315258-14048994)x3 copy number gain See cases [RCV000052909] Chr19:10315258..14048994 [GRCh38]
Chr19:10425934..14159806 [GRCh37]
Chr19:10286934..14020806 [NCBI36]
Chr19:19p13.2-13.12
pathogenic
GRCh38/hg38 19p13.2-13.12(chr19:12132052-14751798)x3 copy number gain See cases [RCV000052910] Chr19:12132052..14751798 [GRCh38]
Chr19:12242867..14862610 [GRCh37]
Chr19:12103867..14723610 [NCBI36]
Chr19:19p13.2-13.12
pathogenic

Additional Information

Database Acc Id Source(s)
COSMIC LOC117125597 COSMIC
GTEx LOC117125597 GTEx
Human Proteome Map LOC117125597 Human Proteome Map
NCBI Gene LOC117125597 ENTREZGENE