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LOC126806870 CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:165592326-165593525 [ Homo sapiens (human) ]

Gene ID: 126806870, updated on 12-Sep-2024

Summary

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Gene symbol
LOC126806870
Gene description
CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:165592326-165593525
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 region 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, where it was defined as a group 2 enhancer that depends on the BRD2, BRD4, P300/CBP, MED14 and CDK7 cofactors, with strong dependence on CDK7. A subregion was also validated as an enhancer by ChIP-STARR-seq in primed human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. [provided by RefSeq, Dec 2022]
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Genomic context

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See LOC126806870 in Genome Data Viewer
Location:
chromosome: 3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (165874538..165875737)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (168657623..168658822)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (165592326..165593525)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1322 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:165177431-165178630 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:165290391-165290985 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:165431125-165431624 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:165438516-165439016 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:165439017-165439517 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20770 Neighboring gene Sharpr-MPRA regulatory region 7963 Neighboring gene butyrylcholinesterase Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:165702256-165702834 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:165743989-165744490 Neighboring gene uncharacterized LOC124909497 Neighboring gene MT-ND4L pseudogene 10 Neighboring gene MT-ND4 pseudogene 17

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. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, 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

  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:165592369-165592892

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_083190.1 

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

    Range
    165874538..165875737
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    168657623..168658822
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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