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LOC127406512 NANOG-H3K27ac hESC enhancer GRCh37_chr6:56708226-56709093 [ Homo sapiens (human) ]

Gene ID: 127406512, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127406512
Gene description
NANOG-H3K27ac hESC enhancer GRCh37_chr6:56708226-56709093
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 histone modification. This locus also includes three accessible chromatin subregions that were validated as silencers based on their 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 LOC127406512 in Genome Data Viewer
Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (56843379..56844408)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (56684991..56686013)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (56708177..56709206)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene collagen type XXI alpha 1 chain Neighboring gene NANOG hESC enhancer GRCh37_chr6:56142823-56143330 Neighboring gene NANOG hESC enhancer GRCh37_chr6:56144052-56144553 Neighboring gene dihydrofolate reductase pseudogene 6 Neighboring gene regulator of chromosome condensation 2 pseudogene 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:56399527-56400028 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:56400029-56400528 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:56406989-56407754 Neighboring gene MPRA-validated peak5860 silencer Neighboring gene dystonin Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24702 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24703 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:56579434-56579994 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:56579995-56580556 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:56581759-56582299 Neighboring gene NANOG hESC enhancer GRCh37_chr6:56616684-56617267 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17296 Neighboring gene NANOG hESC enhancer GRCh37_chr6:56624276-56624832 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24704 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:56640200-56641045 Neighboring gene MPRA-validated peak5861 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:56707357-56708225 Neighboring gene Sharpr-MPRA regulatory region 11401 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24705 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_92361 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24706 Neighboring gene DST antisense RNA 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_92363 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_92364 Neighboring gene ribosomal protein L17 pseudogene 26 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24707 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:56803197-56804396 Neighboring gene RNA, U6 small nuclear 626, pseudogene

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 17297
  • ATAC-STARR-seq lymphoblastoid silent region 17298
  • ATAC-STARR-seq lymphoblastoid silent region 17299

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_108483.2 

    Range
    101..1130
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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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    56843379..56844408
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    56684991..56686013
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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