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LOC112840921 BRD4-independent group 4 enhancer GRCh37_chr2:26685720-26686919 [ Homo sapiens (human) ]

Gene ID: 112840921, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112840921
Gene description
BRD4-independent group 4 enhancer GRCh37_chr2:26685720-26686919
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 8:EnhW, candidate weak enhancer and open chromatin) and K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 7:EnhWF, candidate poised/weak enhancer; flanking open chromatin of candidate enhancers). [provided by RefSeq, Aug 2022]
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Genomic context

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Location:
2p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (26462852..26464051)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (26501483..26502682)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (26686489..26686783)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene adhesion G protein-coupled receptor F3 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:26568936-26569703 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15471 Neighboring gene selenoprotein I Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15472 Neighboring gene dynein regulatory complex subunit 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:26680500-26681070 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:26681071-26681640 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:26683329-26684034 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15473 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:26703326-26703826 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:26704893-26705698 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:26712674-26712916 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15474 Neighboring gene otoferlin Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11274 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:26728504-26729004 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:26734217-26735140 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:26744163-26744328 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:26759696-26760624 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:26760625-26761553 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:26765926-26766660 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:26780985-26781778 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:26781779-26782571 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:26785229-26785729 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:26788976-26789481 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:26799126-26799700 Neighboring gene ciliary microtubule inner protein 2C Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:26813715-26814459 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:26814460-26815203 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:26821036-26821536 Neighboring gene calcium and integrin binding family member 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:26856058-26856598

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 888

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_060956.2 

    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    26462852..26464051
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    26501483..26502682
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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