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LOC127405685 NANOG-H3K27ac hESC enhancer GRCh37_chr6:29634655-29635264 [ Homo sapiens (human) ]

Gene ID: 127405685, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127405685
Gene description
NANOG-H3K27ac hESC enhancer GRCh37_chr6:29634655-29635264
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 in naive and primed human embryonic stem cells, where it associates with the NANOG transcription factor and is marked by the H3K27ac histone modification. 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 K562 erythroleukemia cells. [provided by RefSeq, Jun 2023]
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Genomic context

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See LOC127405685 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 (29666878..29667487)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (29541568..29542177)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (29634655..29635264)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene gamma-aminobutyric acid type B receptor subunit 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:29589456-29590006 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:29590007-29590556 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:29592149-29592734 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:29596552-29597357 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:29598769-29599270 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:29610193-29610692 Neighboring gene SUMO2 pseudogene 1 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:29616349-29616969 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:29622853-29623353 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:29627633-29628069 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:29628451-29629365 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:29629366-29630280 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:29630281-29631194 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:29634045-29634654 Neighboring gene myelin oligodendrocyte glycoprotein Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:29647510-29648030 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:29648031-29648552 Neighboring gene ZFP57 zinc finger protein Neighboring gene ReSE screen-validated silencer GRCh37_chr6:29671001-29671115 Neighboring gene zinc finger DHHC-type containing 20 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. Systematic identification of silencers in human cells. Pang B, et al. Nat Genet, 2020 Mar. PMID 32094911, 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

  • ReSE screen-validated silencer GRCh37_chr6:29634968-29635177

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_107656.1 

    Range
    101..710
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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
    29666878..29667487
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_167244.2 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    932582..933191
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

  1. NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

    Range
    1153343..1153952
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_3

Genomic

  1. NT_167245.2 Reference GRCh38.p14 ALT_REF_LOCI_3

    Range
    932419..933029
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_4

Genomic

  1. NT_167246.2 Reference GRCh38.p14 ALT_REF_LOCI_4

    Range
    931991..932601
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_5

Genomic

  1. NT_167247.2 Reference GRCh38.p14 ALT_REF_LOCI_5

    Range
    932256..932865
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_6

Genomic

  1. NT_167248.2 Reference GRCh38.p14 ALT_REF_LOCI_6

    Range
    932374..932984
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_7

Genomic

  1. NT_167249.2 Reference GRCh38.p14 ALT_REF_LOCI_7

    Range
    975909..976518
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    29541568..29542177
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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