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LOC123620088 Sharpr-MPRA regulatory region 8162 [ Homo sapiens (human) ]

Gene ID: 123620088, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123620088
Gene description
Sharpr-MPRA regulatory region 8162
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. The major subregion was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay in primed human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. Another subregion was validated as a repressive element by Sharpr-MPRA (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 20:ReprD, Polycomb repression w. Duke DNase/promoter and conservation enriched). [provided by RefSeq, Jan 2023]
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Genomic context

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Location:
6p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (33769776..33770446)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (33590956..33591626)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (33737929..33738223)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ubiquinol-cytochrome c reductase complex assembly factor 2 Neighboring gene uncharacterized LOC124901304 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33678073-33678970 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24368 Neighboring gene Sharpr-MPRA regulatory region 11056 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:33692274-33693024 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33695430-33696209 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33696210-33696988 Neighboring gene inositol hexakisphosphate kinase 3 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:33703405-33703659 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33710674-33711363 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33711622-33712515 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33712516-33713408 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33713409-33714302 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33718585-33719144 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33719703-33720261 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33728947-33729550 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17054 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17055 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33740622-33741320 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33747376-33748316 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33748317-33749256 Neighboring gene LEM domain nuclear envelope protein 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33750197-33751135 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:33755871-33756420 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17057 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24369 Neighboring gene uncharacterized LOC105375024 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33758333-33758936 Neighboring gene motilin

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. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, 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

  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33737553-33738087

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_078072.2 

    Range
    101..771
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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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    33769776..33770446
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    33590956..33591626
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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