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LOC127892669 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:17948150-17948904 [ Homo sapiens (human) ]

Gene ID: 127892669, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127892669
Gene description
NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:17948150-17948904
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 and 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 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 LOC127892669 in Genome Data Viewer
Location:
chromosome: 20
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (17967507..17968261)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (18018630..18019384)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (17948150..17948904)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17568 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:17887704-17887865 Neighboring gene RNA, U6 small nuclear 192, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:17909901-17910427 Neighboring gene MPRA-validated peak4160 silencer Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:17919356-17919949 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17570 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:17921137-17921728 Neighboring gene sorting nexin 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17572 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17573 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:17948905-17949659 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr20:17950167-17951366 Neighboring gene small nucleolar RNA, C/D box 17 Neighboring gene mitochondrial genome maintenance exonuclease 1 Neighboring gene NANOG hESC enhancer GRCh37_chr20:17964055-17965008 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17579 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:17980569-17981070 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:17985803-17986364 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17580 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:17988051-17988612 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:17988613-17989173 Neighboring gene prothymosin alpha pseudogene 3

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 17574

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_142461.1 

    Range
    101..855
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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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    17967507..17968261
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    18018630..18019384
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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