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LOC123477741 H3K27ac-H3K4me1 hESC enhancers GRCh37_chr4:49272361-49273132 and GRCh37_chr4:49273133-49273904 [ Homo sapiens (human) ]

Gene ID: 123477741, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123477741
Gene description
H3K27ac-H3K4me1 hESC enhancers GRCh37_chr4:49272361-49273132 and GRCh37_chr4:49273133-49273904
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. Two subregions marked by the H3K27ac and H3K4me1 histone modifications were validated as active enhancers by ChIP-STARR-seq in human embryonic stem cells. An overlapping subregion was also validated as a functional repressive element 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 Repressive non-DNase unmatched - State 20:ReprD, Polycomb repression w. Duke DNase/promoter and conservation enriched) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 25:Art, potential CNV or repetitive artifacts). [provided by RefSeq, Oct 2022]
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Genomic context

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Location:
4p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (49270344..49271887)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (49229186..49230729)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (49272909..49273203)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene MT-CO3 pseudogene 39 Neighboring gene MT-ND3 pseudogene 22 Neighboring gene translation initiation factor IF-2-like Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:49336410-49336910 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:49336911-49337411 Neighboring gene ankyrin repeat domain 20 family member A17, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:49512008-49512508 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:49512509-49513009 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:49516310-49516810 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:49516811-49517311 Neighboring gene translation initiation factor IF-2-like Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:49525865-49526381

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. 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

  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:49272361-49273132
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:49273133-49273904
  • Sharpr-MPRA regulatory region 1861

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_077544.2 

    Range
    101..1644
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    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    49270344..49271887
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_021159991.1 Reference GRCh38.p14 PATCHES

    Range
    195623..197166
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    49229186..49230729
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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