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LOC113875026 H3K4me1 hESC enhancers GRCh37_chrX:42201990-42202490 and GRCh37_chrX:42202491-42202991 [ Homo sapiens (human) ]

Gene ID: 113875026, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113875026
Gene description
H3K4me1 hESC enhancers GRCh37_chrX:42201990-42202490 and GRCh37_chrX:42202491-42202991
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 H3K4me1 histone modification were validated as active enhancers by ChIP-STARR-seq in naive human embryonic stem cells. An overlapping subregion was also validated as an enhancer 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 Activating DNase matched - State 3:PromF, promoter flanking). [provided by RefSeq, Nov 2022]
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Genomic context

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Location:
Xp
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (42342738..42343739)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (41748040..41749041)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (42202309..42202603)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 630, pseudogene Neighboring gene RNA, U6 small nuclear 1124, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:42325954-42326454 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:42333231-42333767 Neighboring gene ribosomal biogenesis factor-like Neighboring gene uncharacterized LOC124905181

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

  • H3K4me1 hESC enhancer GRCh37_chrX:42201990-42202490
  • H3K4me1 hESC enhancer GRCh37_chrX:42202491-42202991
  • Sharpr-MPRA regulatory region 2101

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_063214.2 

    Range
    101..1102
    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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    42342738..42343739
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    41748040..41749041
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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