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LOC127885883 hESC enhancers GRCh37_chr17:16117644-16118560 and GRCh37_chr17:16118561-16119476 [ Homo sapiens (human) ]

Gene ID: 127885883, updated on 27-Aug-2024

Summary

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Gene symbol
LOC127885883
Gene description
hESC enhancers GRCh37_chr17:16117644-16118560 and GRCh37_chr17:16118561-16119476
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 includes two enhancers that were validated by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in human embryonic stem cells, where both are marked by the H3K27ac histone modification, and one additionally associates with the NANOG transcription factor and is marked by H3K4me1. 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, Jun 2023]
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Genomic context

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Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (16214330..16216162)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (16116641..16118473)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene nuclear receptor corepressor 1 Neighboring gene small nucleolar RNA, C/D box 163 Neighboring gene RNA, 7SL, cytoplasmic 442, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11748 Neighboring gene phosphatidylinositol glycan anchor biosynthesis class L Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11749 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11750 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:16189057-16190046 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11752 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11753 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11754 Neighboring gene microRNA 1288 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:16208527-16209028 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8217 Neighboring gene centromere protein V

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 11747
  • ATAC-STARR-seq lymphoblastoid silent region 8216
  • H3K27ac hESC enhancer GRCh37_chr17:16117644-16118560
  • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:16118561-16119476

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_135618.2 

    Range
    101..1933
    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    16214330..16216162
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    16116641..16118473
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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