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LOC127399527 H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:194407453-194407958 [ Homo sapiens (human) ]

Gene ID: 127399527, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127399527
Gene description
H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:194407453-194407958
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 and H3K4me1 histone modifications. 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 LOC127399527 in Genome Data Viewer
Location:
chromosome: 3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (194686713..194687229)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (197383291..197383807)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (194407442..194407958)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374291 Neighboring gene transmembrane protein 44 Neighboring gene Sharpr-MPRA regulatory region 9326 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:194339883-194340383 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:194343378-194343921 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15026 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:194356897-194357398 Neighboring gene TMEM44 antisense RNA 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21031 Neighboring gene MPRA-validated peak4980 silencer Neighboring gene large 60S subunit nuclear export GTPase 1 Neighboring gene uncharacterized LOC124909474 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:194395226-194396425 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21032 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21033 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:194407959-194408462 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15028 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21034 Neighboring gene uncharacterized LOC105374292 Neighboring gene family with sequence similarity 43 member A Neighboring gene long intergenic non-protein coding RNA 1968 Neighboring gene Sharpr-MPRA regulatory region 10974 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21035 Neighboring gene Sharpr-MPRA regulatory region 1010 Neighboring gene MPRA-validated peak4981 silencer Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:194470908-194471615 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:194471765-194471953 Neighboring gene family with sequence similarity 151 member A pseudogene Neighboring gene long intergenic non-protein coding RNA 1972

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 within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. 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

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 15027

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_101493.2 

    Range
    101..617
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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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    194686713..194687229
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    197383291..197383807
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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