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LOC127894188 H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61583471-61584300 [ Homo sapiens (human) ]

Gene ID: 127894188, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127894188
Gene description
H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61583471-61584300
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 LOC127894188 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 (62952119..62952948)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (64752242..64753071)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (61583471..61584300)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:61517086-61517616 Neighboring gene small nucleolar RNA, H/ACA box 117 Neighboring gene death inducer-obliterator 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61531289-61532143 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13130 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:61553829-61554340 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:61556733-61557346 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:61557347-61557960 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61558843-61559691 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18219 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13133 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13134 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13135 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61569565-61570233 Neighboring gene GID complex subunit 8 homolog Neighboring gene solute carrier family 17 member 9 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13141 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13140 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61604715-61605564 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr20:61605565-61606416 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18220 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61613574-61614491 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61629479-61630243 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:61630758-61631400 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:61631401-61632042 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:61635197-61635710 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61638035-61638740 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61638741-61639448 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18221 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13142 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13143 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18222 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18223 Neighboring gene basic helix-loop-helix family member e23 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61648125-61649092 Neighboring gene uncharacterized LOC105372718

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 13138
  • ATAC-STARR-seq lymphoblastoid silent region 13139

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_143877.1 

    Range
    101..930
    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    62952119..62952948
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    64752242..64753071
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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