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LOC112486218 Sharpr-MPRA regulatory region 11460 [ Homo sapiens (human) ]

Gene ID: 112486218, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112486218
Gene description
Sharpr-MPRA regulatory region 11460
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 12:CtcfO, distal CTCF/candidate insulator with open chromatin), with weaker activity in K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 12:CtcfO). [provided by RefSeq, Jul 2021]
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Genomic context

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See LOC112486218 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 (88194063..88194357)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (94262336..94262630)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (88227669..88227963)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88146853-88147354 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88147355-88147854 Neighboring gene uncharacterized LOC400553 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:88150297-88151496 Neighboring gene zinc finger protein 469 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88181294-88181921 Neighboring gene uncharacterized LOC105371401 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88220489-88221296 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88228172-88228704 Neighboring gene long intergenic non-protein coding RNA 2182 Neighboring gene Sharpr-MPRA regulatory region 6305 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88275942-88276442 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88292312-88293058 Neighboring gene uncharacterized LOC107984862 Neighboring gene uncharacterized LOC124900374 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88294229-88295094 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:88298191-88299390 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88305120-88305626 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88308260-88309065 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88337429-88337930 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88338969-88339468 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88342417-88342918 Neighboring gene Sharpr-MPRA regulatory region 14328 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:88366225-88367424 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88383362-88384329 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88447094-88447638 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88448183-88448726 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88463994-88464796 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:88476410-88477609 Neighboring gene uncharacterized LOC112268182

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_056862.1 

    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    88194063..88194357
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    94262336..94262630
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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