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LOC127269201 H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:53387115-53387797 [ Homo sapiens (human) ]

Gene ID: 127269201, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127269201
Gene description
H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:53387115-53387797
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 was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in naive human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. 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 phorbol 12-myristate 13-acetate-treated (for megakaryocytic differentiation) K562 erythroleukemia 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) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, Jun 2023]
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Genomic context

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See LOC127269201 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (52921443..52922125)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (52802959..52803636)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (53387115..53387797)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene zyg-11 family member B, cell cycle regulator Neighboring gene Sharpr-MPRA regulatory region 11599 Neighboring gene RNA, U6 small nuclear 969, pseudogene Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:53297677-53298444 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:53301449-53302130 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:53302131-53302812 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 899 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:53309013-53309606 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:53334860-53335744 Neighboring gene zyg-11 family member A, cell cycle regulator Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:53335745-53336627 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:53370741-53371532 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:53372219-53372718 Neighboring gene Sharpr-MPRA regulatory region 4702 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:53377381-53377881 Neighboring gene translation machinery-associated protein 7-like Neighboring gene enoyl-CoA hydratase domain containing 2 Neighboring gene ATP synthase membrane subunit j pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 901 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:53393043-53393558 Neighboring gene sterol carrier protein 2 Neighboring gene H3 histone pseudogene 2

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 silent region 900
  • ReSE screen-validated silencer GRCh37_chr1:53387132-53387310

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_091062.1 

    Range
    101..783
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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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    52921443..52922125
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    52802959..52803636
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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