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LOC112694712 BRD4-independent group 4 enhancer GRCh37_chr20:4055096-4056295 [ Homo sapiens (human) ]

Gene ID: 112694712, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112694712
Gene description
BRD4-independent group 4 enhancer GRCh37_chr20:4055096-4056295
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 an active enhancer by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay in HCT116 colorectal carcinoma cells. This sequence was defined as a group 4 enhancer that depends on the BRD2, P300/CBP, MED14 and CDK7 cofactors, but it has limited or no dependence on the BRD4 bromodomain protein. A subregion was also validated as a functional enhancer by Sharpr-MPRA (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 20:ReprD, Polycomb repression with Duke DNase/promoter and conservation enriched) and K562 erythroleukemia cells (group: K562 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Aug 2022]
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Genomic context

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Location:
20p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (4074449..4075648)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (4105885..4107084)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (4055709..4056003)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:4014121-4014765 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17491 Neighboring gene ferritin light chain pseudogene 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:4026722-4027222 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:4027223-4027723 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:4043892-4044780 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:4052097-4052598 Neighboring gene ribosomal protein L21 pseudogene 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:4052599-4053098 Neighboring gene CRISPRi-validated cis-regulatory element chr20.311 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:4089506-4090058 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:4090059-4090610 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:4090944-4091508 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr20:4115669-4116868 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:4129207-4130148 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:4130149-4131090 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12638 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_60212 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:4138284-4138784 Neighboring gene uncharacterized LOC124904861 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:4141411-4142344 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:4148169-4148870 Neighboring gene spermine oxidase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12639 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12640 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12641 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:4175883-4176064 Neighboring gene long intergenic non-protein coding RNA 1433

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. Differential cofactor dependencies define distinct types of human enhancers. Neumayr C, et al. Nature, 2022 Jun. PMID 35650434, Free PMC Article
  2. 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)

General gene information

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Other Names

  • Sharpr-MPRA regulatory region 12382

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_060742.2 

    Range
    101..1300
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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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    4074449..4075648
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    4105885..4107084
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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