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LOC112340390 H3K27ac hESC enhancer GRCh37_chr16:23549829-23550328 [ Homo sapiens (human) ]

Gene ID: 112340390, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112340390
Gene description
H3K27ac hESC enhancer GRCh37_chr16:23549829-23550328
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 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 K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 14:Gen5', transcription transition, highly expressed genes towards 5' end), with weaker activity in HepG2 liver carcinoma cells (group: HepG2 Activating non-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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See LOC112340390 in Genome Data Viewer
Location:
16p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (23538508..23539007)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (23814290..23814788)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (23549929..23550223)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene golgi associated, gamma adaptin ear containing, ARF binding protein 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:23511811-23512473 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:23515779-23516280 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:23516281-23516780 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7276 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7277 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7278 Neighboring gene cyclin Y like 7 (pseudogene) Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10582 Neighboring gene glutamyl-tRNA synthetase 2, mitochondrial Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:23549327-23549828 Neighboring gene SUB1 pseudogene 4 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:23567356-23568000 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10583 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:23568645-23569289 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:23569290-23569933 Neighboring gene ubiquitin family domain containing 1 Neighboring gene NADH:ubiquinone oxidoreductase subunit AB1 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:23605373-23605549 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7281

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 duplications and other features in 12 Mb of DNA sequence from human chromosome 16p and 16q. Loftus BJ, et al. Genomics, 1999 Sep 15. PMID 10493829
  2. 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
  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

  • Sharpr-MPRA regulatory region 1793

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_056789.2 

    Range
    101..600
    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    23538508..23539007
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    23814290..23814788
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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