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LOC127894167 H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61435960-61436865 [ Homo sapiens (human) ]

Gene ID: 127894167, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127894167
Gene description
H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61435960-61436865
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 naive human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. This locus also includes three 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 LOC127894167 in Genome Data Viewer
Location:
chromosome: 20
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (62804608..62805558)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (64603580..64604524)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (61435960..61436910)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372716 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:61424450-61425144 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18214 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13119 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61426422-61426968 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13120 Neighboring gene MRG domain binding protein Neighboring gene OGFR antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13124 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13125 Neighboring gene opioid growth factor receptor Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:61446582-61447268 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61447957-61448642 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61449331-61450016 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61450017-61450704 Neighboring gene collagen type IX alpha 3 chain Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61454586-61455274 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61455275-61455962 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13126 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61461792-61462748 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61462749-61463704 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61463705-61464661 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61464662-61465617 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr20:61467141-61468340 Neighboring gene transcription factor like 5 Neighboring gene diphthamide biosynthesis 3 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 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 13121
  • ATAC-STARR-seq lymphoblastoid silent region 13122
  • ATAC-STARR-seq lymphoblastoid silent region 13123

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_143861.2 

    Range
    101..1051
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    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    62804608..62805558
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    64603580..64604524
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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