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LOC127404035 H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:139494224-139494861 [ Homo sapiens (human) ]

Gene ID: 127404035, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127404035
Gene description
H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:139494224-139494861
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 and H3K4me1 histone modifications. 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 LOC127404035 in Genome Data Viewer
Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (140114639..140115276)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (140639735..140640372)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (139494224..139494861)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16433 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16434 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16435 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:139259501-139260264 Neighboring gene neuregulin 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16436 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23254 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16437 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23255 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:139364881-139366080 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23256 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23257 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23258 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:139422349-139423018 Neighboring gene uncharacterized LOC124900193 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23259 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16440 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16441 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16442 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:139487907-139488408 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16443 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16444 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23260 Neighboring gene mitosis associated long intergenic non-coding RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:139525474-139526020 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:139526021-139526567 Neighboring gene purine rich element binding protein A Neighboring gene uncharacterized LOC124901086 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:139533596-139534255 Neighboring gene uncharacterized LOC101929719 Neighboring gene IgA inducing protein

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 23261

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_105984.1 

    Range
    101..738
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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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    140114639..140115276
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    140639735..140640372
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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