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LOC112806057 BRD4-independent group 4 enhancer GRCh37_chr2:165370742-165371941 [ Homo sapiens (human) ]

Gene ID: 112806057, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112806057
Gene description
BRD4-independent group 4 enhancer GRCh37_chr2:165370742-165371941
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 HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region), with weaker activity in K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Aug 2022]
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Genomic context

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See LOC112806057 in Genome Data Viewer
Location:
2q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (164514232..164515431)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (164971553..164972752)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (165371029..165371323)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16725 Neighboring gene phosphoribosyl pyrophosphate synthetase 1 pseudogene 1 Neighboring gene cytochrome P450 family 2 subfamily C member 56, pseudogene Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:165227718-165228219 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:165315134-165316001 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:165316002-165316868 Neighboring gene growth factor receptor bound protein 14 Neighboring gene EIF3E pseudogene 3 Neighboring gene cordon-bleu WH2 repeat protein like 1 Neighboring gene small nucleolar RNA, H/ACA box 70F

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 9133

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_060910.2 

    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
    164514232..164515431
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    164971553..164972752
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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