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LOC112163525 Sharpr-MPRA regulatory region 2968 [ Homo sapiens (human) ]

Gene ID: 112163525, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112163525
Gene description
Sharpr-MPRA regulatory region 2968
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 HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 8:EnhW, candidate weak enhancer and open chromatin), with weaker activity in K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 22:ReprW, weaker Polycomb repression). [provided by RefSeq, Jul 2021]
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Genomic context

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See LOC112163525 in Genome Data Viewer
Location:
12q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (114738864..114739158)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (114715936..114716230)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (115176669..115176963)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene TBX3 antisense RNA 1 Neighboring gene uncharacterized LOC105369999 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:115173261-115174104 Neighboring gene small nucleolar RNA SNORA27 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:115223243-115223742 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:115237130-115237630 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:115237631-115238131 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:115253275-115253775 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:115255288-115255810 Neighboring gene uncharacterized LOC124903079 Neighboring gene uncharacterized LOC124903080

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_056550.1 

    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    114738864..114739158
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    114715936..114716230
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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