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LOC125371454 H3K27ac hESC enhancer GRCh37_chr19:3969519-3970148 [ Homo sapiens (human) ]

Gene ID: 125371454, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125371454
Gene description
H3K27ac hESC enhancer GRCh37_chr19:3969519-3970148
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 sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay in primed human embryonic stem cells, where it is marked by the H3K27ac histone modification. A subregion was also validated as a repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 1:Tss, active promoter, TSS/CpG island region). [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC125371454 in Genome Data Viewer
Location:
19p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (3969521..3970150)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (3948777..3949406)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3938329-3939088 Neighboring gene nicotinamide riboside kinase 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3951361-3952130 Neighboring gene death associated protein kinase 3 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3970149-3970780 Neighboring gene microRNA 637 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9864 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13746 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3981471-3982322 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3984027-3984878 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9865 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13748 Neighboring gene eukaryotic translation elongation factor 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3987713-3988214 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3988215-3988714 Neighboring gene small nucleolar RNA, C/D box 37 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3998837-3999482 Neighboring gene H3K27ac hESC enhancers GRCh37_chr19:4006760-4007651 and GRCh37_chr19:4007652-4008542 Neighboring gene protein inhibitor of activated STAT 4

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. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, 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

  • Sharpr-MPRA regulatory region 11828

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_080724.2 

    Range
    101..730
    Download
    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
    3969521..3970150
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    3948777..3949406
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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