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LOC121740652 Sharpr-MPRA regulatory region 10125 [ Homo sapiens (human) ]

Gene ID: 121740652, updated on 12-Sep-2024

Summary

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Gene symbol
LOC121740652
Gene description
Sharpr-MPRA regulatory region 10125
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 the Sharpr-MPRA technique (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 5:Enh, candidate strong enhancer, open chromatin) and K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 21:Repr, strong Polycomb repression). [provided by RefSeq, Jun 2021]
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Genomic context

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See LOC121740652 in Genome Data Viewer
Location:
6p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (53643471..53643765)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (53483402..53483696)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (53508269..53508563)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:53437832-53438332 Neighboring gene KRT19 interacting long noncoding RNA in hepatocellular carcinoma Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:53480209-53481408 Neighboring gene long intergenic non-protein coding RNA 1564 Neighboring gene Sharpr-MPRA regulatory region 14005 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24699 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24700 Neighboring gene kelch like family member 31 Neighboring gene Sharpr-MPRA regulatory region 11274 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:53587553-53587738 Neighboring gene uncharacterized LOC124901334 Neighboring gene NANOG hESC enhancer GRCh37_chr6:53595032-53595549 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:53599001-53600200 Neighboring gene uncharacterized LOC124901333

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

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)

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_075714.1 

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

    Range
    53643471..53643765
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    53483402..53483696
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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