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LOC127268849 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:40506053-40506687 [ Homo sapiens (human) ]

Gene ID: 127268849, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127268849
Gene description
NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:40506053-40506687
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 includes an enhancer that was validated 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 three 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, Jun 2023]
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Genomic context

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See LOC127268849 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 (40040349..40041028)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (39909669..39910348)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (40506021..40506700)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene MYCL antisense RNA 1 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:40363871-40364442 Neighboring gene Sharpr-MPRA regulatory region 6057 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 714 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 715 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 716 Neighboring gene MYCL proto-oncogene, bHLH transcription factor Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:40409912-40410434 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 717 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 823 Neighboring gene MFSD2 lysolipid transporter A, lysophospholipid Neighboring gene ribosomal protein S2 pseudogene 12 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:40446045-40446898 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 718 Neighboring gene uncharacterized LOC105378669 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 719 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 824 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:40505419-40506052 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:40518723-40519222 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:40524580-40525341 Neighboring gene cyclase associated actin cytoskeleton regulatory protein 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:40535511-40536710 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 720 Neighboring gene Sharpr-MPRA regulatory region 13734 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 829 Neighboring gene palmitoyl-protein thioesterase 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:40598557-40599056 Neighboring gene OAZ1 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. 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 825
  • ATAC-STARR-seq lymphoblastoid active region 826
  • ATAC-STARR-seq lymphoblastoid active region 827

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_090710.2 

    Range
    101..780
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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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    40040349..40041028
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    39909669..39910348
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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