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LOC112540018 Sharpr-MPRA regulatory region 10665 [ Homo sapiens (human) ]

Gene ID: 112540018, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112540018
Gene description
Sharpr-MPRA regulatory region 10665
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, May 2018]
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Genomic context

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See LOC112540018 in Genome Data Viewer
Location:
18p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (3060651..3060945)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (3216193..3216487)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (3060649..3060943)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene lipin 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13033 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13034 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13035 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:2998944-2999866 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr18:3003878-3004395 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9251 Neighboring gene small nuclear ribonucleoprotein polypeptide C pseudogene 4 Neighboring gene small nucleolar RNA SNORA70 Neighboring gene Sharpr-MPRA regulatory region 4192 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:3051522-3052022 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13036 Neighboring gene myomesin 1 Neighboring gene RNA, U7 small nuclear 25 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13037 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13038 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13039 Neighboring gene Sharpr-MPRA regulatory region 2253 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13040 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9252 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13041 Neighboring gene MYL12A and MYL12B antisense RNA 1 Neighboring gene myosin light chain 12A

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_057369.1 

    Range
    101..395
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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_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    3060651..3060945
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    3216193..3216487
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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