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LOC127405229 H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:5085857-5086546 [ Homo sapiens (human) ]

Gene ID: 127405229, updated on 10-Oct-2023

Summary

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Gene symbol
LOC127405229
Gene description
H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:5085857-5086546
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 primed human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. This locus also includes three 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 LOC127405229 in Genome Data Viewer
Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (5085543..5086312)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (4954751..4955520)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901248 Neighboring gene LYRM4 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:5027971-5028470 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:5031032-5031192 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:5044856-5046055 Neighboring gene LYR motif containing 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23899 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23900 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:5063575-5064076 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16866 Neighboring gene TFB2M pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16867 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16868 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16869 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23901 Neighboring gene protein phosphatase 1 regulatory subunit 3G Neighboring gene MPRA-validated peak5632 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:5130070-5130656 Neighboring gene Sharpr-MPRA regulatory region 2533 Neighboring gene microRNA 3691 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:5193017-5193524 Neighboring gene Sharpr-MPRA regulatory region 15549 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:5230418-5231617 Neighboring gene uncharacterized LOC124901249

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 across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. 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 silent region 16870
  • ATAC-STARR-seq lymphoblastoid silent region 16871
  • ATAC-STARR-seq lymphoblastoid silent region 16872

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_107200.2 

    Range
    101..870
    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    5085543..5086312
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    4954751..4955520
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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