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LOC122889024 H3K4me1 hESC enhancer GRCh37_chr3:8664536-8665156 [ Homo sapiens (human) ]

Gene ID: 122889024, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122889024
Gene description
H3K4me1 hESC enhancer GRCh37_chr3:8664536-8665156
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 in naive human embryonic stem cells, where it is marked by the H3K4me1 histone modification. A subregion was also validated as a repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). An accessible chromatin subregion was used in a lentiviral ReSE (repressive ability of silencer elements) screen that assays for cell survival based on transcriptional repression of an apoptosis-inducing fusion protein. That subregion was identified as a functional silencer in HepG2 cells. [provided by RefSeq, Jun 2023]
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Genomic context

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Location:
3p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (8622850..8623666)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (8614217..8615033)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (8664589..8664883)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene LMCD1 antisense RNA 1 Neighboring gene uncharacterized LOC107986010 Neighboring gene RNA, U4atac small nuclear 17, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:8413440-8413972 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:8413973-8414503 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:8453270-8453770 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:8482473-8482990 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:8497791-8498357 Neighboring gene Sharpr-MPRA regulatory region 2381 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:8540163-8541096 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:8541097-8542030 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:8577298-8578266 Neighboring gene LIM and cysteine rich domains 1 Neighboring gene uncharacterized LOC107986009 Neighboring gene long intergenic non-protein coding RNA 312 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:8652364-8653245 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:8653246-8654126 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19390 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19391 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19392 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19393 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14028 Neighboring gene ssu-2 homolog Neighboring gene MPRA-validated peak4531 silencer Neighboring gene olfactory receptor family 7 subfamily E member 122 pseudogene Neighboring gene NANOG hESC enhancer GRCh37_chr3:8765327-8765828 Neighboring gene caveolin 3 Neighboring gene oxytocin receptor

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. Systematic identification of silencers in human cells. Pang B, et al. Nat Genet, 2020 Mar. PMID 32094911, Free PMC Article
  2. 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
  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

  • ReSE screen-validated silencer GRCh37_chr3:8664973-8665352
  • Sharpr-MPRA regulatory region 1018

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_077156.3 

    Range
    101..917
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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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    8622850..8623666
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    8614217..8615033
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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