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LOC127397617 H3K27ac hESC enhancer GRCh37_chr3:52443693-52444241 [ Homo sapiens (human) ]

Gene ID: 127397617, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127397617
Gene description
H3K27ac hESC enhancer GRCh37_chr3:52443693-52444241
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 primed human embryonic stem cells, where it is marked by the H3K27ac histone modification. This locus also includes two accessible chromatin subregions that were validated as silencers based on their 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 LOC127397617 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 (52409677..52410674)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (52442658..52443655)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (52443693..52444690)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:52332967-52333837 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:52333838-52334707 Neighboring gene glycerate kinase Neighboring gene microRNA 135a-1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:52344635-52345552 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19940 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:52350849-52351787 Neighboring gene dynein axonemal heavy chain 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:52377569-52378070 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:52385639-52386434 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:52396307-52396860 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14440 Neighboring gene protein phosphatase 2 regulatory subunit B'gamma pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:52443144-52443692 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14443 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19941 Neighboring gene BRCA1 associated deubiquitinase 1 Neighboring gene VISTA enhancer hs2179 Neighboring gene PHD finger protein 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:52471583-52472088 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:52478216-52479092 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:52479093-52479969 Neighboring gene semaphorin 3G Neighboring gene Sharpr-MPRA regulatory region 2927 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:52486099-52486919 Neighboring gene troponin C1, slow skeletal and cardiac type

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 14441
  • ATAC-STARR-seq lymphoblastoid silent region 14442

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_099586.2 

    Range
    101..1098
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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
    52409677..52410674
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    52442658..52443655
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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