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LOC127267941 OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:20987241-20988160 [ Homo sapiens (human) ]

Gene ID: 127267941, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127267941
Gene description
OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:20987241-20988160
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 associates with the OCT4 and NANOG transcription factors and is marked by the H3K27ac and H3K4me1 histone modifications. This locus also includes an accessible chromatin subregion that was validated as a silencer based on its 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 LOC127267941 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 (20660748..20661714)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (20486935..20487901)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (20987241..20988207)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene microRNA 6084 Neighboring gene PTEN induced kinase 1 Neighboring gene PINK1 antisense RNA Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:20988161-20989080 Neighboring gene dolichyl-diphosphooligosaccharide--protein glycosyltransferase non-catalytic subunit Neighboring gene kinesin family member 17 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21011543-21012044 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21015049-21015549 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:21015960-21016182 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 368 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21036574-21037228 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 369 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 370 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:21054065-21054727 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:21054728-21055389 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21056983-21057676 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21057677-21058368 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21058590-21059262 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21059263-21059933 Neighboring gene SH2 domain containing 5 Neighboring gene heterochromatin protein 1 binding protein 3 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:21112523-21112715 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 375 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 376

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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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 367

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_089802.2 

    Range
    101..1067
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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
    20660748..20661714
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    20486935..20487901
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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