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LOC123480940 H3K4me1 hESC enhancer GRCh37_chr4:140746169-140746710 [ Homo sapiens (human) ]

Gene ID: 123480940, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123480940
Gene description
H3K4me1 hESC enhancer GRCh37_chr4:140746169-140746710
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 was validated as an active enhancer 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 both HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 21:Repr, strong Polycomb repression) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 21:Repr). [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC123480940 in Genome Data Viewer
Location:
4q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (139825015..139825556)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (143144671..143145212)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (140746329..140746623)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene mastermind like transcriptional coactivator 3 Neighboring gene uncharacterized LOC124900782 Neighboring gene RN7SK pseudogene 253 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:140736907-140737476 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:140737477-140738044 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:140746711-140747251 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:140753881-140754399 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:140796336-140797059 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21931 Neighboring gene Sharpr-MPRA regulatory region 6454 Neighboring gene uncharacterized LOC105377452 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:140884299-140884498 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21932 Neighboring gene uncharacterized LOC124900783 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr4:140969917-140970453 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr4:140970454-140970989

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

  • Sharpr-MPRA regulatory region 693

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_077634.2 

    Range
    101..642
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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
    139825015..139825556
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    143144671..143145212
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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