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LOC111946236 Sharpr-MPRA regulatory region 2775 [ Homo sapiens (human) ]

Gene ID: 111946236, updated on 17-Sep-2024

Summary

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Gene symbol
LOC111946236
Gene description
Sharpr-MPRA regulatory region 2775
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, Feb 2018]
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Genomic context

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See LOC111946236 in Genome Data Viewer
Location:
10p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (4947777..4948071)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (4948109..4948403)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (4989969..4990263)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376375 Neighboring gene uncharacterized LOC105376374 Neighboring gene NANOG hESC enhancer GRCh37_chr10:4857623-4858270 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2078 Neighboring gene Sharpr-MPRA regulatory region 4775 Neighboring gene aldo-keto reductase family 1 member E2 Neighboring gene CRISPRi-validated cis-regulatory element chr10.180 Neighboring gene Sharpr-MPRA regulatory region 12277 Neighboring gene NANOG hESC enhancer GRCh37_chr10:4912837-4913364 Neighboring gene aldo-keto reductase family 1 member C6, pseudogene Neighboring gene CRISPRi-validated cis-regulatory element chr10.185 Neighboring gene uncharacterized LOC124902365 Neighboring gene aldo-keto reductase family 1 member C1 Neighboring gene uncharacterized LOC101928051 Neighboring gene aldo-keto reductase family 1 member C2

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_056325.1 

    Range
    101..395
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    4947777..4948071
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    4948109..4948403
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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Other Literature Sources
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