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LOC112296179 Sharpr-MPRA regulatory region 10228 [ Homo sapiens (human) ]

Gene ID: 112296179, updated on 10-Dec-2024

Summary

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Gene symbol
LOC112296179
Gene description
Sharpr-MPRA regulatory region 10228
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 5:Enh, candidate strong enhancer, open chromatin), with weaker activation in K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 6:EnhF, candidate strong enhancer, flanking open chromatin). [provided by RefSeq, Apr 2018]
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Genomic context

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See LOC112296179 in Genome Data Viewer
Location:
16p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (10626012..10626306)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (10661939..10662233)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (10719869..10720163)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1290 Neighboring gene Sharpr-MPRA regulatory region 3744 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10381 Neighboring gene epithelial membrane protein 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10382 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:10658085-10658281 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:10672481-10673058 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7193 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:10677994-10679193 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:10688146-10688662 Neighboring gene Sharpr-MPRA regulatory region 2211 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10383 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:10715105-10715806 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10384 Neighboring gene tektin 5 Neighboring gene uncharacterized LOC105371079 Neighboring gene MT-CYB pseudogene 33

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_056764.1 

    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    10626012..10626306
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    10661939..10662233
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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