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LOC127401006 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:76649872-76650791 [ Homo sapiens (human) ]

Gene ID: 127401006, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127401006
Gene description
NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:76649872-76650791
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 primed human embryonic stem cells, where it associates with the NANOG transcription factor and is marked by the H3K27ac and H3K4me1 histone modifications. An accessible chromatin subregion was used in a lentiviral ReSE (repressive ability of silencer elements) screen that assays for cell survival based on transcriptional repression of an apoptosis-inducing fusion protein. That subregion was identified as a functional silencer in phorbol 12-myristate 13-acetate-treated (for megakaryocytic differentiation) K562 erythroleukemia cells. This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate 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, Jun 2023]
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Genomic context

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See LOC127401006 in Genome Data Viewer
Location:
chromosome: 4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (75724688..75725607)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (79064816..79065735)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (76649872..76650791)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene cytochrome c oxidase subunit 6C pseudogene 9 Neighboring gene cyclin dependent kinase like 2 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:76597475-76598452 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21620 Neighboring gene G3BP stress granule assembly factor 2 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:76599431-76600408 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:76600409-76601385 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15481 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21621 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:76627962-76628708 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:76630201-76630946 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:76641306-76641821 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:76648951-76649871 Neighboring gene USO1 vesicle transport factor Neighboring gene uncharacterized LOC105377284 Neighboring gene RNA, U2 small nuclear 16, pseudogene Neighboring gene uncharacterized LOC105377285 Neighboring gene Sharpr-MPRA regulatory region 11706 Neighboring gene protein phosphatase with EF-hand domain 2

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. Systematic identification of silencers in human cells. Pang B, et al. Nat Genet, 2020 Mar. PMID 32094911, Free PMC Article
  2. 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
  3. 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 21622
  • ReSE screen-validated silencer GRCh37_chr4:76650052-76650229

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_102969.1 

    Range
    101..1020
    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    75724688..75725607
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    79064816..79065735
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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