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LOC113146419 Sharpr-MPRA regulatory region 1984 [ Homo sapiens (human) ]

Gene ID: 113146419, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113146419
Gene description
Sharpr-MPRA regulatory region 1984
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 a functional enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 1:Tss, active promoter, TSS/CpG island region) and 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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Location:
6q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (142146992..142147286)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (143339084..143339378)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (142468129..142468423)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986654 Neighboring gene MPRA-validated peak6171 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:142409105-142409658 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:142409659-142410210 Neighboring gene neuromedin B receptor Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:142468581-142469101 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:142476776-142477403 Neighboring gene gap junction protein epsilon 1 Neighboring gene vesicle trafficking 1 Neighboring gene Sharpr-MPRA regulatory region 15423 Neighboring gene long intergenic non-protein coding RNA 2919 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:142596514-142597713 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17614 Neighboring gene Sharpr-MPRA regulatory region 14737 Neighboring gene adhesion G protein-coupled receptor G6 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:142695388-142695989 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:142695947-142697146 Neighboring gene Sharpr-MPRA regulatory regions 3748 and 6738

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 25176

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_061646.1 

    Range
    101..395
    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    142146992..142147286
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    143339084..143339378
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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