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LOC127268269 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27114367-27115193 [ Homo sapiens (human) ]

Gene ID: 127268269, updated on 10-Oct-2023

Summary

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Gene symbol
LOC127268269
Gene description
NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27114367-27115193
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 (MPRA) in primed 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, one of which was validated as an enhancer and the other as a silencer based on their ability to activate or 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 LOC127268269 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (26787876..26788702)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (26625831..26626657)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101928728 Neighboring gene translation initiation factor IF-2-like Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:27019176-27019690 Neighboring gene hESC enhancers GRCh37_chr1:27021339-27022275 and GRCh37_chr1:27022276-27023211 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 489 Neighboring gene Sharpr-MPRA regulatory region 12508 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:27033907-27034406 Neighboring gene AT-rich interaction domain 1A Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27048400-27048980 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27048981-27049560 Neighboring gene heart enhancer 10 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:27051301-27051880 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27051881-27052460 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:27057943-27058472 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 490 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 517 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:27098665-27099864 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 518 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 519 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 521 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 522 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27130608-27131323 Neighboring gene phosphatidylinositol glycan anchor biosynthesis class V Neighboring gene RNA, 7SL, cytoplasmic 165, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr1:27152961-27153113 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 493 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 523 Neighboring gene zinc finger DHHC-type palmitoyltransferase 18 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 524 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 525 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:27179723-27180224 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:27181471-27181643

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

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 520
  • ATAC-STARR-seq lymphoblastoid silent region 491

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_090130.1 

    Range
    101..927
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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
    26787876..26788702
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    26625831..26626657
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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