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LOC111946250 Sharpr-MPRA regulatory region 10071 [ Homo sapiens (human) ]

Gene ID: 111946250, updated on 17-Sep-2024

Summary

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Gene symbol
LOC111946250
Gene description
Sharpr-MPRA regulatory region 10071
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 both HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 4:PromP, inactive/poised promoter, highly conserved) and K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 2:TssF, active promoter, flanking TSS/CpG islands). [provided by RefSeq, Feb 2018]
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Genomic context

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See LOC111946250 in Genome Data Viewer
Location:
10q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (67763471..67763765)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (68631922..68632216)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (69523229..69523523)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene catenin alpha 3 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_15807 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_15830 Neighboring gene microRNA 7151 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_15959 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_15994 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3449 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16073 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3455 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3454 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3453 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3452 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3451 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3450 Neighboring gene tRNA-Ser (anticodon TGA) 1-1 Neighboring gene aldo-keto reductase family 1 member B10 pseudogene 1 Neighboring gene ribosomal protein L21 pseudogene 92

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_056339.1 

    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
    67763471..67763765
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    68631922..68632216
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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Other Literature Sources
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