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LOC112533646 Sharpr-MPRA regulatory region 4378 [ Homo sapiens (human) ]

Gene ID: 112533646, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112533646
Gene description
Sharpr-MPRA regulatory region 4378
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. The major subregion 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. 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 matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC112533646 in Genome Data Viewer
Location:
17q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (48522127..48522791)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (49385560..49386224)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (46599489..46599783)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene src kinase associated phosphoprotein 1 Neighboring gene uncharacterized LOC101927166 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12331 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:46560473-46561672 Neighboring gene uncharacterized LOC124904019 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12332 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr17:46593890-46594400 Neighboring gene uncharacterized LOC105371808 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr17:46597283-46597974 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr17:46597975-46598664 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:46608263-46608843 Neighboring gene Sharpr-MPRA regulatory region 4554 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:46620694-46621339 Neighboring gene HOXB cluster antisense RNA 1 Neighboring gene homeobox B1 Neighboring gene homeobox B2

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

  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:46599631-46600153

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_056917.2 

    Range
    101..765
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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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    48522127..48522791
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    49385560..49386224
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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