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LOC111365184 NANOG-H3K27ac hESC enhancer GRCh37_chr7:24517479-24518142 [ Homo sapiens (human) ]

Gene ID: 111365184, updated on 10-Oct-2023

Summary

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Gene symbol
LOC111365184
Gene description
NANOG-H3K27ac hESC enhancer GRCh37_chr7:24517479-24518142
Gene type
biological region
Feature type(s)
regulatory: enhancer, transcriptional_cis_regulatory_region
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 predicted to be a cell type-specific enhancer based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. The major subregion was validated as an active enhancer by ChIP-STARR-seq in primed human embryonic stem cells, where it associates with the NANOG transcription factor and is marked by the H3K27ac histone modification. An overlapping subregion was also validated as a functional enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin), with weaker activation in K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 8:EnhW, candidate weak enhancer and open chromatin). Another subregion also functioned as an enhancer by high-throughput massively parallel reporter assays (MPRAs) in HepG2 cells. The same subregion contains a conserved motif for the NFE2L2 activator, and mutation of that motif results in reduced enhancer activity. [provided by RefSeq, Oct 2022]
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Genomic context

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Location:
7p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (24477830..24478523)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (24615816..24616509)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (24517449..24517743)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986777 Neighboring gene small nucleolar RNA U13 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:24317744-24318943 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:24365511-24365721 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:24383660-24384160 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:24388531-24389031 Neighboring gene neuropeptide Y Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:24435498-24436157 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:24436158-24436818 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:24438272-24438926 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:24440891-24441545 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr7:24441546-24442200 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25741 Neighboring gene NANOG hESC enhancer GRCh37_chr7:24446236-24446807 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:24466273-24466844 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:24466845-24467415 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:24472530-24473088 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:24474463-24475000 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25742 Neighboring gene uncharacterized LOC124901601 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr7:24516814-24517478 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:24518143-24518806 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:24518807-24519469 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:24562031-24562238 Neighboring gene RNA, U6 small nuclear 1103, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25743 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25744 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:24613275-24613774 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25746 Neighboring gene NANOG hESC enhancer GRCh37_chr7:24615771-24616272 Neighboring gene SUMO2 pseudogene 14 Neighboring gene protein associated with LIN7 2, MAGUK p55 family member

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 dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay. Kheradpour P, et al. Genome Res, 2013 May. PMID 23512712, Free PMC Article
  2. Mapping and analysis of chromatin state dynamics in nine human cell types. Ernst J, et al. Nature, 2011 May 5. PMID 21441907, Free PMC Article
  3. Toward a complete human genome sequence. Sanger Center, et al. Genome Res, 1998 Nov. PMID 9847074
  4. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, Free PMC Article
  5. 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 variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • NFE2L2 activator MPRA enhancer 39
  • NFE2L2 motif-containing MPRA enhancer 39
  • Sharpr-MPRA regulatory region 8696
  • massively parallel reporter assay enhancer 39

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_055797.3 

    Range
    101..794
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    24477830..24478523
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    24615816..24616509
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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