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LOC127815022 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:84303773-84304487 [ Homo sapiens (human) ]

Gene ID: 127815022, updated on 10-Oct-2023

Summary

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Gene symbol
LOC127815022
Gene description
NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:84303773-84304487
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 primed human embryonic stem cells, where it associates with the NANOG transcription factor 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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Location:
chromosome: 9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (81688858..81689794)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (93840928..93841862)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene CST complex subunit TEN1-like Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr9:84138078-84139277 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr9:84164162-84164662 Neighboring gene VISTA enhancer hs1118 Neighboring gene uncharacterized LOC105376106 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:84207247-84208446 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:84210105-84210800 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr9:84210801-84211494 Neighboring gene NANOG hESC enhancer GRCh37_chr9:84236633-84237248 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr9:84237249-84237864 Neighboring gene NANOG hESC enhancer GRCh37_chr9:84238663-84239186 Neighboring gene TLE family member 1, transcriptional corepressor Neighboring gene VISTA enhancer hs1359 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:84278031-84278532 Neighboring gene Sharpr-MPRA regulatory region 9381 Neighboring gene Sharpr-MPRA regulatory region 7656 Neighboring gene VISTA enhancer hs556 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19976 Neighboring gene TLE1 divergent transcript Neighboring gene ReSE screen-validated silencer GRCh37_chr9:84349086-84349247 Neighboring gene RNA, U6 small nuclear 1035, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:84375421-84375922 Neighboring gene NANOG hESC enhancer GRCh37_chr9:84398794-84399306 Neighboring gene NANOG hESC enhancer GRCh37_chr9:84434914-84435503 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr9:84458661-84459441 Neighboring gene RNA, 5S ribosomal pseudogene 287

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 across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. 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

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 19975

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_116540.2 

    Range
    101..1037
    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    81688858..81689794
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    93840928..93841862
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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