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LOC117125594 H3K27ac-H3K4me1 hESC enhancers GRCh37_chr19:13001481-13002118 and GRCh37_chr19:13002119-13002756 [ Homo sapiens (human) ]

Gene ID: 117125594, updated on 12-Sep-2024

Summary

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Gene symbol
LOC117125594
Gene description
H3K27ac-H3K4me1 hESC enhancers GRCh37_chr19:13001481-13002118 and GRCh37_chr19:13002119-13002756
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer, transcriptional_cis_regulatory_region
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic region was predicted to have enhancer function 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. Two subregions marked by the H3K27ac and H3K4me1 histone modifications were validated as active enhancers by ChIP-STARR-seq in primed human embryonic stem cells. Another subregion was validated as a positively-acting cis-regulatory element for the KLF1 (Kruppel like factor 1) gene based on CRISPR/Cas9-mediated perturbation (CRISPRi-FlowFISH method) in K562 erythroleukemia cells. An accessible chromatin subregion was 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 HepG2 liver carcinoma cells. [provided by RefSeq, Jun 2023]
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Genomic context

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See LOC117125594 in Genome Data Viewer
Location:
19p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (12890667..12891942)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (13015119..13016394)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (13001481..13002756)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene deoxyribonuclease 2, lysosomal Neighboring gene CRISPRi-FlowFISH-validated KLF1 regulatory element 1 Neighboring gene CRISPRi-FlowFISH-validated DNASE2 regulatory element 1 Neighboring gene CRISPRi-FlowFISH-validated DNASE2 regulatory element 2 Neighboring gene CRISPRi-FlowFISH-validated PRDX2 and RAD23A regulatory element Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10180 Neighboring gene CRISPRi-FlowFISH-validated CALR, DHPS, JUNB, PRDX2, RAD23A, RNASEH2A and WDR83OS regulatory element Neighboring gene CRISPRi-FlowFISH-validated KLF1 regulatory element 2 Neighboring gene KLF transcription factor 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14090 Neighboring gene glutaryl-CoA dehydrogenase Neighboring gene ribosomal protein S6 pseudogene 25 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr19:13010146-13011345 Neighboring gene synaptonemal complex central element protein 2 Neighboring gene CRISPRi-FlowFISH-validated KLF1 regulatory element 3 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:13021591-13021759 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:13022560-13023262 Neighboring gene Sharpr-MPRA regulatory region 4901 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14092

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations. Fulco CP, et al. Nat Genet, 2019 Dec. PMID 31784727, Free PMC Article
  2. Systematic identification of silencers in human cells. Pang B, et al. Nat Genet, 2020 Mar. PMID 32094911, Free PMC Article
  3. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, Free PMC Article

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • CRISPRi-FlowFISH-validated KLF1 regulatory element
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:13001481-13002118
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:13002119-13002756
  • ReSE screen-validated silencer GRCh37_chr19:13001524-13001782

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_068132.2 

    Range
    101..1376
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    12890667..12891942
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    13015119..13016394
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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