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LOC127897080 NANOG-H3K27ac hESC enhancer GRCh37_chrX:2807746-2808337 [ Homo sapiens (human) ]

Gene ID: 127897080, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127897080
Gene description
NANOG-H3K27ac hESC enhancer GRCh37_chrX:2807746-2808337
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 (MPRA) in naive human embryonic stem cells, where it associates with the NANOG transcription factor and is marked by the H3K27ac histone modification. This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate 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 LOC127897080 in Genome Data Viewer
Location:
chromosome: X
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (2889705..2890296)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (2502202..2502793)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (2807746..2808337)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:2699593-2700274 Neighboring gene Xg glycoprotein (Xg blood group) Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:2700956-2701636 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:2701637-2702317 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:2711950-2712538 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:2717356-2718298 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:2718299-2719240 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:2721222-2721887 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chrX:2722445-2723644 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:2764748-2764850 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:2766248-2766874 Neighboring gene glycogenin 2 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:2809856-2810546 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:2815103-2815898 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:2815899-2816694 Neighboring gene ARSD antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:2841876-2842386 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:2842387-2842896 Neighboring gene arylsulfatase D Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20638 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20639 Neighboring gene arylsulfatase L Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:2878567-2879390 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:2879391-2880216 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:2881867-2882690 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29373

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 active region 29372

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_146569.1 

    Range
    101..692
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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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    2889705..2890296
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    2502202..2502793
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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