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LOC127402159 H3K27ac hESC enhancer GRCh37_chr5:218445-219253 [ Homo sapiens (human) ]

Gene ID: 127402159, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127402159
Gene description
H3K27ac hESC enhancer GRCh37_chr5:218445-219253
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 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. 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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See LOC127402159 in Genome Data Viewer
Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (218131..219138)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (209174..210181)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (218246..219253)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene NANOG hESC enhancer GRCh37_chr5:99879-100414 Neighboring gene pleckstrin homology and RhoGEF domain containing G4B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:137535-138040 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:159786-160286 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:160287-160787 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr5:169157-170356 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:170845-171358 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:171359-171872 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:181876-182376 Neighboring gene Sharpr-MPRA regulatory region 15179 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22268 Neighboring gene Sharpr-MPRA regulatory region 11960 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22269 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22270 Neighboring gene uncharacterized LOC124900929 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:207882-208207 Neighboring gene leucine rich repeat containing 14B Neighboring gene coiled-coil domain containing 127 Neighboring gene succinate dehydrogenase complex flavoprotein subunit A Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:270110-270802 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22271 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15861 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:278988-279488 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:279489-279989 Neighboring gene PDCD6-AHRR readthrough (NMD candidate) Neighboring gene PDCD6 divergent transcript Neighboring gene programmed cell death 6 Neighboring gene PPP4R2 pseudogene 1

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 silent region 15859
  • ATAC-STARR-seq lymphoblastoid silent region 15860

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_104118.2 

    Range
    101..1108
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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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    218131..219138
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    209174..210181
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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