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LOC113839512 Sharpr-MPRA regulatory region 2041 [ Homo sapiens (human) ]

Gene ID: 113839512, updated on 4-Mar-2025

Summary

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Gene symbol
LOC113839512
Gene description
Sharpr-MPRA regulatory region 2041
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. A subregion was validated as a functional 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 1:Tss, active promoter, TSS/CpG island region), with weak activation in HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 1:Tss). This locus also includes an accessible chromatin subregion that was validated as a silencer based on its ability to repress 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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See LOC113839512 in Genome Data Viewer
Location:
9q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (127786170..127786584)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (139993621..139994035)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (130548449..130548863)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene SH2 domain containing 3C Neighboring gene uncharacterized LOC107987132 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:130539526-130539796 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29049 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29050 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:130545551-130545741 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29052 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20310 Neighboring gene Sharpr-MPRA regulatory region 7866 Neighboring gene microRNA 2861 Neighboring gene microRNA 3960 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29053 Neighboring gene cyclin dependent kinase 9 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20313 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130571111-130571753 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130571754-130572397 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130572398-130573040 Neighboring gene folylpolyglutamate synthase Neighboring gene uncharacterized LOC102723566 Neighboring gene endoglin

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 within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. PMID 35858748, 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 silent region 20312

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_063129.2 

    Range
    101..515
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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
    127786170..127786584
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    139993621..139994035
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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