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LOC127271472 OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:210547305-210548216 [ Homo sapiens (human) ]

Gene ID: 127271472, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127271472
Gene description
OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:210547305-210548216
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 and primed human embryonic stem cells, where it associates with the OCT4 and NANOG transcription factors and is marked by the H3K27ac histone modification. 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 LOC127271472 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 (210373961..210374872)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (209612625..209613536)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (210547305..210548216)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904502 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:210484426-210485625 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_3009 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1779 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2478 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_3018 Neighboring gene uncharacterized LOC124904503 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:210546392-210547304 Neighboring gene Sharpr-MPRA regulatory region 10816 Neighboring gene hedgehog acyltransferase Neighboring gene RNA, U5A small nuclear 8, pseudogene Neighboring gene BPNT2 pseudogene 1 Neighboring gene Sharpr-MPRA regulatory region 9170 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:210770524-210771385 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:210771386-210772246 Neighboring gene Sharpr-MPRA regulatory region 1701 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2479 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2480 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:210863521-210864021 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2481 Neighboring gene uncharacterized LOC105372901 Neighboring gene MPRA-validated peak678 silencer Neighboring gene MPRA-validated peak679 silencer Neighboring gene potassium voltage-gated channel subfamily H member 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 1780

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_093324.1 

    Range
    101..1012
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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
    210373961..210374872
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_011332687.1 Reference GRCh38.p14 PATCHES

    Range
    153703..154614
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    209612625..209613536
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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