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LOC121740633 NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr5:176559765-176560316 and GRCh37_chr5:176560317-176560870 [ Homo sapiens (human) ]

Gene ID: 121740633, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121740633
Gene description
NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr5:176559765-176560316 and GRCh37_chr5:176560317-176560870
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 sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. Two adjacent subregions were validated as enhancers by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in primed human embryonic stem cells, where they associate with the NANOG transcription factor and are marked by the H3K27ac and H3K4me1 histone modifications. Another subregion was validated as an 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 non-DNase unmatched - State 10:DNaseD, primarily Duke DNase, candidate regulatory elements in more likely repressive locations). 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, Jun 2023]
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Genomic context

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See LOC121740633 in Genome Data Viewer
Location:
5q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (177132764..177133869)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (177675974..177677079)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (176559809..176560103)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:176449401-176449938 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:176449939-176450475 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16670 Neighboring gene zinc finger protein 346 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:176488686-176489885 Neighboring gene FGFR4 5' regulatory region Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176537235-176537734 Neighboring gene fibroblast growth factor receptor 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23693 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176558105-176558658 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:176560871-176561422 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:176561423-176561976 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16676 Neighboring gene nuclear receptor binding SET domain protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176692158-176693050 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176693051-176693942 Neighboring gene ribosomal protein L21 pseudogene 60 Neighboring gene protein arginine methyltransferase 1 pseudogene 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. 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
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. 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 variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 16673
  • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176559765-176560316
  • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176560317-176560870
  • Sharpr-MPRA regulatory region 75

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_075695.3 

    Range
    101..1206
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    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    177132764..177133869
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    177675974..177677079
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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