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LOC125177497 Sharpr-MPRA regulatory region 8372 [ Homo sapiens (human) ]

Gene ID: 125177497, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125177497
Gene description
Sharpr-MPRA regulatory region 8372
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer
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 a repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 7:EnhWF, candidate poised/weak enhancer, flanking open chromatin of candidate enhancers). [provided by RefSeq, Jan 2023]
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Genomic context

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Location:
17q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (48003088..48003677)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (48864901..48865490)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:46033917-46034862 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:46034863-46035808 Neighboring gene proline rich 15 like Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8645 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:46048841-46049468 Neighboring gene CDK5 regulatory subunit associated protein 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:46052765-46053265 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:46072377-46072975 Neighboring gene uncharacterized LOC124904017 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12321 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8646 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:46092391-46092892 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:46092893-46093392 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12322 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8647 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:46103594-46104152 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:46104153-46104709 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:46105093-46105359 Neighboring gene COPI coat complex subunit zeta 2 Neighboring gene microRNA 10226

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

General gene information

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Other Names

  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:46080454-46081008

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_080552.2 

    Range
    101..690
    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    48003088..48003677
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    48864901..48865490
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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