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LOC112272546 Sharpr-MPRA regulatory region 7830 [ Homo sapiens (human) ]

Gene ID: 112272546, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112272546
Gene description
Sharpr-MPRA regulatory region 7830
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. 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 HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin). It also displayed weak repressive activity by Sharpr-MPRA in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Mar 2018]
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Genomic context

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Location:
14q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (62692171..62692465)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (56899152..56899446)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (63158889..63159183)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105370529 Neighboring gene uncharacterized LOC105370528 Neighboring gene NANOG hESC enhancer GRCh37_chr14:63033845-63034401 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:63102949-63103450 Neighboring gene ATP synthase F1 subunit alpha pseudogene 4 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_34896 Neighboring gene potassium voltage-gated channel subfamily H member 5 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr14:63248008-63248579 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_34948 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:63511437-63511940 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:63511941-63512444 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr14:63527728-63528286 Neighboring gene LINE-1 retrotransposable element ORF1 protein-like Neighboring gene poly(ADP-ribose) polymerase 1 pseudogene 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

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_056685.1 

    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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    62692171..62692465
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    56899152..56899446
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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