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LOC121529655 H3K27ac hESC enhancer GRCh37_chr14:89883272-89883804 [ Homo sapiens (human) ]

Gene ID: 121529655, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121529655
Gene description
H3K27ac hESC enhancer GRCh37_chr14:89883272-89883804
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 sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It includes an enhancer that was validated by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in naive human embryonic stem cells, where it is marked by the H3K27ac histone modification. A subregion was also validated as an enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Activating DNase matched - State 4:PromP, inactive/poised promoter, highly conserved). This locus also includes two accessible chromatin subregions that were validated as silencers based on their ability to 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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Location:
14q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (89416928..89417614)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (83640647..83641333)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (89883429..89883723)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene forkhead box N3 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:89760189-89760856 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:89760857-89761524 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:89762398-89762960 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:89762961-89763522 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:89763523-89764084 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8850 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8851 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8852 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8853 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:89775236-89775736 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8854 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:89775737-89776237 Neighboring gene cyclase associated actin cytoskeleton regulatory protein 2 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8856 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8857 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8858 Neighboring gene Sharpr-MPRA regulatory region 10244 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:89807187-89807686 Neighboring gene uncharacterized LOC101928817 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5998 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:89818959-89819674 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8859 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8860 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8861 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8863 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8862 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8864 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8865 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8866 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:89858093-89858593 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:89865667-89866237 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:89869264-89869764 Neighboring gene Sharpr-MPRA regulatory region 4092 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:89882738-89883271 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:89891172-89891786 Neighboring gene uncharacterized LOC107984635 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr14:89894848-89896047 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr14:89898457-89899010 Neighboring gene FOXN3 antisense RNA 1 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:89906553-89907136 Neighboring gene Sharpr-MPRA regulatory region 349 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr14:89907723-89908306 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:89919266-89920166 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:89929363-89929862 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:89932229-89933148 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:89933149-89934068 Neighboring gene FOXN3 antisense RNA 2

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. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, Free PMC Article
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, Free PMC Article
  3. 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 variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 5999
  • ATAC-STARR-seq lymphoblastoid silent region 6000
  • Sharpr-MPRA regulatory region 4157

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_074767.3 

    Range
    101..787
    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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    89416928..89417614
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    83640647..83641333
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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