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LOC121832824 H3K4me1 hESC enhancer GRCh37_chr11:133800389-133801061 [ Homo sapiens (human) ]

Gene ID: 121832824, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121832824
Gene description
H3K4me1 hESC enhancer GRCh37_chr11:133800389-133801061
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. 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. Another subregion was validated as an enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 20:ReprD, Polycomb repression w. Duke DNase/promoter and conservation enriched), while an overlapping subregion displayed enhancer activity by Sharpr-MPRA in HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 20:ReprD). [provided by RefSeq, Jan 2023]
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Genomic context

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Location:
11q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (133930494..133931166)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (133972710..133973382)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (133800629..133801003)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene calponin 2 pseudogene Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:133764343-133765238 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:133765239-133766134 Neighboring gene microRNA 4697 Neighboring gene immunoglobulin superfamily member 9B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4088 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:133804210-133804968 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:133804969-133805727 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:133809401-133810123 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:133810124-133810845 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:133814904-133815632 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:133816362-133817090 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5767 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:133821059-133821802 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:133821803-133822546 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4089 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:133863530-133864030 Neighboring gene long intergenic non-protein coding RNA 2730 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:133890717-133891220 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:133894031-133894833 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:133896267-133896838 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:133896839-133897409 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:133901031-133901530 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:133902231-133902958 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:133902959-133903686 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:133906753-133907724 Neighboring gene long intergenic non-protein coding RNA 2731

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 3502
  • Sharpr-MPRA regulatory region 9399
  • Sharpr-MPRA regulatory regions 3502 and 9399

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_075899.2 

    Range
    101..773
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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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    133930494..133931166
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    133972710..133973382
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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