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LOC127268167 H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25566071-25566856 [ Homo sapiens (human) ]

Gene ID: 127268167, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127268167
Gene description
H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25566071-25566856
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 primed human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. This locus also includes four accessible chromatin subregions, three of which were validated as enhancers and one as a silencer based on their ability to activate or 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 LOC127268167 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (25239580..25240376)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (25075837..25076633)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (25566071..25566867)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903880 Neighboring gene MPRA-validated peak125 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 448 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 449 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 450 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 451 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25494962-25495462 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25510715-25511215 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25525541-25526040 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:25528106-25528280 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:25554020-25555219 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 452 Neighboring gene uncharacterized LOC124903881 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25559103-25560016 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25565284-25566070 Neighboring gene SYF2 pre-mRNA splicing factor Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25572736-25573460 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:25573461-25574185 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25580071-25580587 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:25580588-25581105 Neighboring gene upstream Rhesus box Neighboring gene arginine and serine rich protein 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:25593225-25593742 Neighboring gene uncharacterized LOC105376882 Neighboring gene Rh blood group D antigen Neighboring gene succinate dehydrogenase complex subunit D pseudogene 6

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 454
  • ATAC-STARR-seq lymphoblastoid active region 455
  • ATAC-STARR-seq lymphoblastoid active region 456
  • ATAC-STARR-seq lymphoblastoid silent region 452

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_090028.2 

    Range
    101..897
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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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    25239580..25240376
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    25075837..25076633
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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