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LOC113839495 Sharpr-MPRA regulatory region 9871 [ Homo sapiens (human) ]

Gene ID: 113839495, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113839495
Gene description
Sharpr-MPRA regulatory region 9871
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. 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 HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 1:Tss, active promoter, TSS/CpG island region), with weaker activation in K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 1:Tss). This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate 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 LOC113839495 in Genome Data Viewer
Location:
9q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (97633289..97633681)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (109805230..109805622)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (100395669..100395963)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancers GRCh37_chr9:100174359-100174860 and GRCh37_chr9:100174861-100175360 Neighboring gene tudor domain containing 7 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr9:100226535-100227734 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28663 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20101 Neighboring gene GATA motif-containing MPRA enhancer 268 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28664 Neighboring gene uncharacterized LOC105376168 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:100278102-100278602 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28665 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28666 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:100293128-100293286 Neighboring gene tropomodulin 1 Neighboring gene Sharpr-MPRA regulatory region 7780 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:100318031-100318532 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:100319241-100319742 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28667 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28668 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:100335093-100335332 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28669 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28670 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28671 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:100396128-100396963 Neighboring gene thiosulfate sulfurtransferase like domain containing 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28674 Neighboring gene nuclear cap binding protein subunit 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28675 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28676 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20102 Neighboring gene XPA, DNA damage recognition and repair factor Neighboring gene keratin 18 pseudogene 13 Neighboring gene papillary thyroid carcinoma susceptibility candidate 2

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 across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. 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 active region 28672

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_063113.2 

    Range
    101..493
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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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    97633289..97633681
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    109805230..109805622
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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