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LOC127890537 H3K27ac hESC enhancer GRCh37_chr19:12904163-12904664 [ Homo sapiens (human) ]

Gene ID: 127890537, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127890537
Gene description
H3K27ac hESC enhancer GRCh37_chr19:12904163-12904664
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer
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 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. This locus also includes three accessible chromatin subregions, two of which were validated as enhancers and one as a silencer based on their ability to activate or repress an origin of replication minimal core promoter by ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) in GM12878 lymphoblastoid cells. Another 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 K562 erythroleukemia cells. [provided by RefSeq, Jun 2023]
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Genomic context

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See LOC127890537 in Genome Data Viewer
Location:
chromosome: 19
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (12793335..12794290)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (12917827..12918782)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (12904149..12905104)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene hook microtubule tethering protein 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14079 Neighboring gene CRISPRi-FlowFISH-validated JUNB regulatory element Neighboring gene microRNA 5684 Neighboring gene CRISPRi-FlowFISH-validated PRDX2 regulatory element 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10173 Neighboring gene JunB proto-oncogene, AP-1 transcription factor subunit Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14082 Neighboring gene peroxiredoxin 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14083 Neighboring gene CRISPRi-FlowFISH-validated RNASEH2A regulatory element Neighboring gene thrombospondin type 1 domain containing 8

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. Systematic identification of silencers in human cells. Pang B, et al. Nat Genet, 2020 Mar. PMID 32094911, Free PMC Article
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. PMID 35858748, 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 Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 14080
  • ATAC-STARR-seq lymphoblastoid active region 14081
  • ATAC-STARR-seq lymphoblastoid silent region 10174
  • ReSE screen-validated silencer GRCh37_chr19:12904899-12905104

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_140464.2 

    Range
    101..1056
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    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
    12793335..12794290
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    12917827..12918782
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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