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LOC127889821 H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:919848-920787 [ Homo sapiens (human) ]

Gene ID: 127889821, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127889821
Gene description
H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:919848-920787
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 and H3K4me1 histone modifications. 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 LOC127889821 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 (919848..920787)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (882587..883526)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (919848..920787)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene MPRA-validated peak3217 silencer Neighboring gene RNA, U6 small nuclear 9 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:904059-904817 Neighboring gene R3H domain containing 4 Neighboring gene Sharpr-MPRA regulatory region 9324 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9627 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9628 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9629 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9630 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:918907-919847 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9633 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9634 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9635 Neighboring gene KISS1 receptor Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9636 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:926209-926969 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:932426-932957 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:932958-933488 Neighboring gene AT-rich interaction domain 3A Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:934552-935082 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9640 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9641 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:947299-947798 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9642 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13576 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:952365-953066 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:953067-953768 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:953750-953958 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:955173-955874 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:956577-957278 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:957654-957846 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:962809-963327 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:965021-965198 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:980065-980655 Neighboring gene HNF4 motif-containing MPRA enhancer 174 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9644 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:983939-984880 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:990841-991786 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9647 Neighboring gene WD repeat domain 18 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:993929-994462 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:994463-994995

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 silent region 9631
  • ATAC-STARR-seq lymphoblastoid silent region 9632

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_139789.1 

    Range
    101..1040
    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
    919848..920787
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    882587..883526
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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