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LOC127397410 H3K27ac hESC enhancer GRCh37_chr3:49026958-49027520 [ Homo sapiens (human) ]

Gene ID: 127397410, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127397410
Gene description
H3K27ac hESC enhancer GRCh37_chr3:49026958-49027520
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 primed 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 an enhancer based on its ability to activate 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 LOC127397410 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 (48989525..48990087)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (49017577..49018139)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (49026958..49027520)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene solute carrier family 25 member 20 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19844 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14341 Neighboring gene hESC enhancers GRCh37_chr3:48955152-48955902 and GRCh37_chr3:48955903-48956654 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:48956655-48957405 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:48959089-48959589 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:48961592-48962092 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:48962093-48962593 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19846 Neighboring gene ARIH2 opposite strand lncRNA Neighboring gene ariadne RBR E3 ubiquitin protein ligase 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19847 Neighboring gene MPRA-validated peak4646 silencer Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:49000975-49001622 Neighboring gene uncharacterized LOC124909376 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:49026394-49026957 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14344 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:49028085-49028646 Neighboring gene uncharacterized LOC124906235 Neighboring gene prolyl 4-hydroxylase, transmembrane Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:49043602-49044590 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14345 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14346 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:49051026-49051863 Neighboring gene WD repeat domain 6 Neighboring gene DALR anticodon binding domain containing 3

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 active region 19848

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_099379.1 

    Range
    101..663
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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
    48989525..48990087
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    49017577..49018139
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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