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LOC112694693 Sharpr-MPRA regulatory region 14145 [ Homo sapiens (human) ]

Gene ID: 112694693, updated on 17-Sep-2024

Summary

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Gene symbol
LOC112694693
Gene description
Sharpr-MPRA regulatory region 14145
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 unmatched - State 9:DNaseU, primarily UW DNase, weaker open chromatin sites) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Jul 2018]
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Genomic context

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See LOC112694693 in Genome Data Viewer
Location:
20p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (23143112..23143406)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (23202323..23202617)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (23123749..23124043)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17627 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17628 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17629 Neighboring gene CD93 molecule Neighboring gene ReSE screen-validated silencer GRCh37_chr20:23097446-23097628 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17630 Neighboring gene long intergenic non-protein coding RNA 656 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr20:23117070-23118269 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr20:23128189-23129388 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:23130883-23131866 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12722 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17631 Neighboring gene long intergenic non-protein coding RNA 3125 Neighboring gene RNA, 5S ribosomal pseudogene 478 Neighboring gene Sharpr-MPRA regulatory region 4869 Neighboring gene MPRA-validated peak4168 silencer Neighboring gene Sharpr-MPRA regulatory region 11415 Neighboring gene Sharpr-MPRA regulatory region 15236 Neighboring gene uncharacterized LOC105372571 Neighboring gene NXT1 antisense RNA 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_060723.1 

    Range
    101..395
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    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    23143112..23143406
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    23202323..23202617
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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