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LOC123775384 Sharpr-MPRA regulatory region 6453 [ Homo sapiens (human) ]

Gene ID: 123775384, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123775384
Gene description
Sharpr-MPRA regulatory region 6453
Gene type
biological region
Feature type(s)
regulatory: 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. It was validated as a functional repressive element by the Sharpr-MPRA technique (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 23:Low, low signal proximal to active elements). [provided by RefSeq, Jan 2022]
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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 (90194630..90194924)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (91406334..91406628)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (90904349..90904643)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene BTB domain and CNC homolog 2 Neighboring gene RN7SK pseudogene 110 Neighboring gene Sharpr-MPRA regulatory region 1684 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:90866227 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:90866333-90867532 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:90883525 Neighboring gene uncharacterized LOC105377890 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:90894000-90895199 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:90927428-90928086 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:90931785-90932984 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:90941289 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24833 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:90981657 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:90982387 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:90995265-90995765 Neighboring gene uncharacterized LOC124901361 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24834 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17397 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17398 Neighboring gene uncharacterized LOC105377891 Neighboring gene NANOG hESC enhancer GRCh37_chr6:91008275-91008776 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:91012867 Neighboring gene microRNA 4464

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_078152.1 

    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
    90194630..90194924
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    91406334..91406628
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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