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LOC127896302 H3K27ac hESC enhancer GRCh37_chr22:39927967-39928482 [ Homo sapiens (human) ]

Gene ID: 127896302, updated on 10-Oct-2023

Summary

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Gene symbol
LOC127896302
Gene description
H3K27ac hESC enhancer GRCh37_chr22:39927967-39928482
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 histone modification. 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, May 2023]
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Genomic context

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See LOC127896302 in Genome Data Viewer
Location:
chromosome: 22
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (39531962..39532477)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (40002592..40003107)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr22:39906581-39907106 Neighboring gene mitochondrial elongation factor 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13758 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19058 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19059 Neighboring gene mitochondrial elongation factor 1 upstream open reading frame Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39919051-39919552 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19060 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19061 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19062 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19063 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19064 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19065 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19066 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19067 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19068 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:39928483-39928998 Neighboring gene Sharpr-MPRA regulatory region 14739 Neighboring gene ribosomal protein S19 binding protein 1 Neighboring gene activating transcription factor 4 Neighboring gene uncharacterized LOC124905120 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39953934-39954532 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39970777-39971278 Neighboring gene calcium voltage-gated channel subunit alpha1 I Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39987813-39988722 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19071 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19072 Neighboring gene Sharpr-MPRA regulatory region 12417 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:40022927-40023476 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:40023477-40024025 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:40030871-40031590 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:40047218-40048148 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:40051895-40052396 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13763 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:40059793-40060322

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. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, Free PMC Article
  2. 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

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 13759

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_145835.1 

    Range
    101..616
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    39531962..39532477
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    40002592..40003107
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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