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LOC113839527 H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132332957-132333820 [ Homo sapiens (human) ]

Gene ID: 113839527, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113839527
Gene description
H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132332957-132333820
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 primed human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. 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 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Jan 2023]
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Genomic context

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Location:
9q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (129570678..129571541)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (141775265..141776128)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (132332969..132333263)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902283 Neighboring gene Sharpr-MPRA regulatory region 12687 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132248797-132249456 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132250117-132250776 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20379 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132252097-132252756 Neighboring gene extensin-like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132252757-132253416 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132253417-132254075 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132256099-132256899 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132256900-132257699 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132257700-132258500 Neighboring gene long intergenic non-protein coding RNA 963 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132258501-132259299 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132259614-132260182 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132260183-132260750 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132287329-132287829 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132310394-132310894 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132317282-132317929 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132318577-132319224 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132319225-132319870 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132320519-132321164 Neighboring gene HNF1 motif-containing MPRA enhancer 89 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132332093-132332956 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132333821-132334682 Neighboring gene uncharacterized LOC105376292 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29113 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132346053-132346610 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29114 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132349961-132350644 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20383 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132362549-132363048 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29115 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132366575-132367074 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132369161-132369798 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20384 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20385 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132373341-132373842 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132373843-132374342 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132382842-132383492 Neighboring gene chromosome 9 open reading frame 50 Neighboring gene N-terminal Xaa-Pro-Lys N-methyltransferase 1

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 9056

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_063138.2 

    Range
    101..964
    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    129570678..129571541
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    141775265..141776128
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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