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LOC127268534 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32110207-32110977 [ Homo sapiens (human) ]

Gene ID: 127268534, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127268534
Gene description
NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32110207-32110977
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 and H3K4me1 histone modifications. This locus also includes two accessible chromatin subregions that were validated as enhancers based on their 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 LOC127268534 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (31644606..31645376)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (31502256..31503026)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (32110207..32110977)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378626 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32041927-32042647 Neighboring gene tubulointerstitial nephritis antigen like 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 571 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:32070860-32072059 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32080194-32080980 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32083206-32083895 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 646 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32090464-32090964 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32090965-32091465 Neighboring gene hypocretin receptor 1 Neighboring gene penta-EF-hand domain containing 1 Neighboring gene PEF1 and COL16A1 antisense RNA 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:32123622-32123860 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32124291-32124792 Neighboring gene collagen type XVI alpha 1 chain Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32131402-32131941 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32131942-32132480 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32133021-32133558 Neighboring gene uncharacterized LOC101929444 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:32145564-32146763 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32147039-32147911 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32162063-32162572 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32164717-32165470 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32166977-32167729 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 572 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 649 Neighboring gene Sharpr-MPRA regulatory region 11964 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32181521-32182116 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32189409-32189910 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 573 Neighboring gene adhesion G protein-coupled receptor B2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 651 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 652 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32218779-32219393 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:32219394-32220007 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32220374-32220980 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32221586-32222191 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32222192-32222796 Neighboring gene microRNA 4254

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 647
  • ATAC-STARR-seq lymphoblastoid active region 648

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_090395.1 

    Range
    101..871
    Download
    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    31644606..31645376
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    31502256..31503026
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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