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LOC127890257 H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:6516143-6516683 [ Homo sapiens (human) ]

Gene ID: 127890257, updated on 10-Oct-2023

Summary

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Gene symbol
LOC127890257
Gene description
H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:6516143-6516683
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 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 a silencer based on its 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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Location:
chromosome: 19
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (6516132..6516703)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (6505633..6506204)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene DENN domain containing 1C Neighboring gene crumbs cell polarity complex component 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6475606-6476345 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6479893-6480392 Neighboring gene Sharpr-MPRA regulatory region 5032 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13825 Neighboring gene tubulin beta 4A class IVa Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9954 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9955 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9956 Neighboring gene CRISPRi-validated cis-regulatory element chr19.1358 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:6506805-6507716 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13827 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13828 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13829 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13830 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13831 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9958 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9959 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13832 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6532416-6532916 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6532917-6533417 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13833 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13834 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13835 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13836 Neighboring gene TNF superfamily member 9 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13837 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13838 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13839 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13840 Neighboring gene TGFBR1 pseudogene 1

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 9957

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_140203.2 

    Range
    101..672
    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
    6516132..6516703
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    6505633..6506204
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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