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LOC112163647 Sharpr-MPRA regulatory region 6807 [ Homo sapiens (human) ]

Gene ID: 112163647, updated on 17-Sep-2024

Summary

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Gene symbol
LOC112163647
Gene description
Sharpr-MPRA regulatory region 6807
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 non-DNase unmatched - State 6:EnhF, candidate strong enhancer, flanking open chromatin) and K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Mar 2018]
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Genomic context

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See LOC112163647 in Genome Data Viewer
Location:
13q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (20506870..20507164)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (19700096..19700390)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (21081009..21081303)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105370102 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr13:20924041-20924563 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr13:20953976-20955175 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:20965718-20966226 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:20966227-20966734 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:20979975-20980494 Neighboring gene NANOG hESC enhancer GRCh37_chr13:20986998-20987499 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:20989417-20989998 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:20989999-20990580 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr13:20993166-20994365 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7418 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7419 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7420 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7421 Neighboring gene crystallin lambda 1 Neighboring gene microRNA 4499 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7422 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7423 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:21067481-21067980 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:21076097-21077093 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5153 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7424 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7425 Neighboring gene Sharpr-MPRA regulatory region 3329 Neighboring gene uncharacterized LOC105370103 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5154 Neighboring gene ReSE screen-validated silencer GRCh37_chr13:21141501-21141689 Neighboring gene intraflagellar transport 88 Neighboring gene solute carrier family 35 member E1 pseudogene 1

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_056624.1 

    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_000013.11 Reference GRCh38.p14 Primary Assembly

    Range
    20506870..20507164
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    19700096..19700390
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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