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LOC127828930 hESC enhancers GRCh37_chr14:105956919-105957662 and GRCh37_chr14:105957663-105958406 [ Homo sapiens (human) ]

Gene ID: 127828930, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127828930
Gene description
hESC enhancers GRCh37_chr14:105956919-105957662 and GRCh37_chr14:105957663-105958406
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 primed human embryonic stem cells, where both are marked by the H3K27ac and H3K4me1 histone modifications and one additionally associates with the OCT4 and NANOG transcription factors. This locus also includes three accessible chromatin subregions, two of which were validated as silencers and one as an enhancer based on their ability to repress or 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 LOC127828930 in Genome Data Viewer
Location:
chromosome: 14
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (105490182..105492069)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (99739550..99741437)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (105956519..105958406)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:105939600-105940132 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6239 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6240 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6241 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6242 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6243 Neighboring gene cysteine rich protein 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:105947154-105947875 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9149 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6245 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6246 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6247 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6248 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:105954409-105954980 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6249 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6250 Neighboring gene cysteine rich protein 1 Neighboring gene tubulin epsilon and delta complex 1 Neighboring gene Sharpr-MPRA regulatory region 9919 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:105974095-105974596 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:105974597-105975096 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:105978261-105978760 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:105986957-105987132 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6253 Neighboring gene transmembrane protein 121 Neighboring gene uncharacterized LOC105370697

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 9150
  • ATAC-STARR-seq lymphoblastoid silent region 6251
  • ATAC-STARR-seq lymphoblastoid silent region 6252
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:105957663-105958406
  • OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:105956919-105957662

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_130426.2 

    Range
    101..1988
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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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    105490182..105492069
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    99739550..99741437
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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