U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC121048736 BRD4-independent group 4 enhancer GRCh37_chr3:196758105-196759304 [ Homo sapiens (human) ]

Gene ID: 121048736, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC121048736
Gene description
BRD4-independent group 4 enhancer GRCh37_chr3:196758105-196759304
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 K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Aug 2022]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See LOC121048736 in Genome Data Viewer
Location:
3q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (197031234..197032433)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (199757505..199758704)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (196758409..196758703)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 2091 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15080 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15081 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15082 Neighboring gene ribosomal protein SA pseudogene 30 Neighboring gene MELTF antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21107 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15083 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:196756444-196757080 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:196757081-196757717 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15084 Neighboring gene melanotransferrin Neighboring gene MPRA-validated peak4992 silencer Neighboring gene discs large MAGUK scaffold protein 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:196860144-196860342 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:196930580-196931118 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15086 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15087 Neighboring gene DLG1 antisense RNA 1 Neighboring gene microRNA 4797

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

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

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

Go to the top of the page Help

Other Names

  • Sharpr-MPRA regulatory region 10918

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_074107.2 

    Range
    101..1300
    Download
    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    197031234..197032433
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    199757505..199758704
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases