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LOC112552154 Sharpr-MPRA regulatory region 2471 [ Homo sapiens (human) ]

Gene ID: 112552154, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112552154
Gene description
Sharpr-MPRA regulatory region 2471
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 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Jun 2018]
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Genomic context

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Location:
19q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (43499097..43499391)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (46319500..46319794)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (44003249..44003543)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene testis expressed 101 Neighboring gene RNA, 28S ribosomal pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr19:43917243-43917429 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14723 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14724 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10717 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:43967981-43968512 Neighboring gene LY6/PLAUR domain containing 3 Neighboring gene pleckstrin homology like domain family B member 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:44008034-44008556 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10719 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:44017305-44017805 Neighboring gene ETHE1 persulfide dioxygenase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10720 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:44029999-44030504 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:44030505-44031009 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10721 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:44035307-44035478 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10722 Neighboring gene zinc finger protein 575

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_059289.1 

    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    43499097..43499391
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    46319500..46319794
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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