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LOC112695093 H3K4me1 hESC enhancer GRCh37_chr22:39544629-39545227 [ Homo sapiens (human) ]

Gene ID: 112695093, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112695093
Gene description
H3K4me1 hESC enhancer GRCh37_chr22:39544629-39545227
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 (MPRA) in primed human embryonic stem cells, where it is marked by the H3K4me1 histone modification. A 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 both HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 9:DNaseU, primarily UW DNase, weaker open chromatin sites) and K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 23:Low, low signal proximal to active elements). This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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Location:
22q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (39148624..39149222)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (39619008..39619612)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (39544889..39545183)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr22:39492371-39493570 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39493781-39494667 Neighboring gene apolipoprotein B mRNA editing enzyme catalytic subunit 3H Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39509973-39510947 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19031 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19032 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13742 Neighboring gene cytochrome c oxidase subunit 5B pseudogene 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39527431-39527992 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39529632-39530316 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39530317-39531000 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39531107-39532084 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39540727-39541516 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13744 Neighboring gene chromobox 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39544030-39544628 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39548263-39548844 Neighboring gene FUN14 domain containing 2 pseudogene 4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39567703-39568508 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39569521-39570190 Neighboring gene Sharpr-MPRA regulatory region 8665 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39601000-39601939 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:39605384-39605884 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39609067-39609686 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39609687-39610305 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr22:39610322-39611521 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39612165-39612782 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39632330-39633224 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39633225-39634119 Neighboring gene platelet derived growth factor subunit B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19036 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13747

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. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, 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

  • ATAC-STARR-seq lymphoblastoid active region 19034
  • Sharpr-MPRA regulatory region 533

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_060871.2 

    Range
    101..699
    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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    39148624..39149222
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    39619008..39619612
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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