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LOC112486215 Sharpr-MPRA regulatory region 3417 [ Homo sapiens (human) ]

Gene ID: 112486215, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112486215
Gene description
Sharpr-MPRA regulatory region 3417
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 10:DNaseD, primarily Duke DNase, candidate regulatory elements in more likely repressive locations) and K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 10:DNaseD). [provided by RefSeq, May 2018]
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Genomic context

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See LOC112486215 in Genome Data Viewer
Location:
16q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (84190903..84191197)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (90256977..90257271)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (84224509..84224803)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene hydroxysteroid dehydrogenase like 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84169151-84169748 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84170943-84171538 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7778 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7779 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7780 Neighboring gene dynein axonemal assembly factor 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:84220503-84221003 Neighboring gene TATA-box binding protein associated factor, RNA polymerase I subunit C Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:84227912-84229111 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84229267-84229889 Neighboring gene splicing factor proline/glutamine-rich Neighboring gene adenosine deaminase domain containing 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84247937-84248438 Neighboring gene potassium voltage-gated channel modifier subfamily G member 4

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_056859.1 

    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    84190903..84191197
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    90256977..90257271
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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