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LOC127891484 H3K27ac hESC enhancer GRCh37_chr19:39339826-39340763 [ Homo sapiens (human) ]

Gene ID: 127891484, updated on 10-Oct-2023

Summary

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Gene symbol
LOC127891484
Gene description
H3K27ac hESC enhancer GRCh37_chr19:39339826-39340763
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 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 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 LOC127891484 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 (38849186..38850123)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (41653243..41654180)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene galectin 4 Neighboring gene MPRA-validated peak3474 silencer Neighboring gene uncharacterized LOC124904712 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr19:39314813-39315370 Neighboring gene enoyl-CoA hydratase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14594 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14595 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:39333551-39334051 Neighboring gene heterogeneous nuclear ribonucleoprotein L Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:39338887-39339825 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14597 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14598 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10586 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:39343185-39343829 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14599 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10587 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:39350790-39350958 Neighboring gene Sharpr-MPRA regulatory region 3140 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:39356343-39356918 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14600 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:39360061-39360631 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:39360661-39361267 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:39361268-39361873 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10589 Neighboring gene Ras and Rab interactor like Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14602 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14603 Neighboring gene sirtuin 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:39384205-39384706

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 10584
  • ATAC-STARR-seq lymphoblastoid silent region 10585

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_141347.1 

    Range
    101..1038
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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
    38849186..38850123
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_014040929.1 Reference GRCh38.p14 PATCHES

    Range
    258858..259795
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    41653243..41654180
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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