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LOC127890089 H3K27ac hESC enhancers GRCh37_chr19:4006760-4007651 and GRCh37_chr19:4007652-4008542 [ Homo sapiens (human) ]

Gene ID: 127890089, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127890089
Gene description
H3K27ac hESC enhancers GRCh37_chr19:4006760-4007651 and GRCh37_chr19:4007652-4008542
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 two enhancers that were validated by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in primed human embryonic stem cells, where they are marked by the H3K27ac histone modification. This locus also includes three accessible chromatin subregions, two of which were validated as silencers and one as an enhancer based on their ability to repress or 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, Jun 2023]
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Genomic context

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See LOC127890089 in Genome Data Viewer
Location:
chromosome: 19
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (4006762..4008544)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (3989021..3990803)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (4006760..4008542)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:3969519-3970148 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3970149-3970780 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9864 Neighboring gene death associated protein kinase 3 Neighboring gene microRNA 637 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 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 eukaryotic translation elongation factor 2 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3998837-3999482 Neighboring gene protein inhibitor of activated STAT 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:4043682-4044414 Neighboring gene zinc finger and BTB domain containing 7A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13750 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9868 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9869 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13751 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9870 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9871 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:4062546-4063053 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13752 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9872 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9873 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9874 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9875 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9876 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9877 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9878 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9880 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9879 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:4068686-4068844 Neighboring gene MPRA-validated peak3265 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13753 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13754 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13755 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:4089732-4090508 Neighboring gene mitogen-activated protein kinase kinase 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13757 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13758 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:4116105-4116291 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9881

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 13749
  • ATAC-STARR-seq lymphoblastoid silent region 9866
  • ATAC-STARR-seq lymphoblastoid silent region 9867
  • H3K27ac hESC enhancer GRCh37_chr19:4006760-4007651
  • H3K27ac hESC enhancer GRCh37_chr19:4007652-4008542

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_140046.2 

    Range
    101..1883
    Download
    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    4006762..4008544
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    3989021..3990803
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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