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LOC127404900 H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:177547789-177548591 [ Homo sapiens (human) ]

Gene ID: 127404900, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127404900
Gene description
H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:177547789-177548591
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 naive human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. This locus also includes four accessible chromatin subregions that were validated as enhancers based on their 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 LOC127404900 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 (178120788..178121590)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (178671028..178671830)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (177547789..177548591)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901147 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23733 Neighboring gene CRISPRi-validated cis-regulatory element chr5.4886 Neighboring gene uncharacterized LOC105377754 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16709 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16710 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16711 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:177541661-177542174 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16712 Neighboring gene NEDD4 binding protein 3 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:177550999-177551800 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:177553540-177554200 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:177554863-177555523 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:177556537-177557188 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:177557189-177557840 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177559119-177559648 Neighboring gene required for meiotic nuclear division 5 homolog B Neighboring gene Sharpr-MPRA regulatory region 11782 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23739 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23740 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177577953-177578454 Neighboring gene NHP2 ribonucleoprotein Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177590971-177591472 Neighboring gene NAD(P)HX epimerase pseudogene

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 23735
  • ATAC-STARR-seq lymphoblastoid active region 23736
  • ATAC-STARR-seq lymphoblastoid active region 23737
  • ATAC-STARR-seq lymphoblastoid active region 23738

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_106845.1 

    Range
    101..903
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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
    178120788..178121590
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    178671028..178671830
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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