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LOC127890365 H3K4me1 hESC enhancer GRCh37_chr19:8570689-8571189 [ Homo sapiens (human) ]

Gene ID: 127890365, updated on 10-Oct-2023

Summary

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Gene symbol
LOC127890365
Gene description
H3K4me1 hESC enhancer GRCh37_chr19:8570689-8571189
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 H3K4me1 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 LOC127890365 in Genome Data Viewer
Location:
chromosome: 19
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (8505792..8506305)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (8493375..8493888)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10024 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10025 Neighboring gene heterogeneous nuclear ribonucleoprotein M Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10026 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13916 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13917 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:8563393-8564079 Neighboring gene PML-RARA regulated adaptor molecule 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10027 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:8571229-8571815 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:8576283-8577173 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10030 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13918 Neighboring gene zinc finger protein 414 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:8587561-8588060 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10031 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:8590637-8591612 Neighboring gene uncharacterized LOC124904633 Neighboring gene myosin IF

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 across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. 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

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 10028
  • ATAC-STARR-seq lymphoblastoid silent region 10029

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_140305.2 

    Range
    101..614
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    8505792..8506305
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    8493375..8493888
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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