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LOC126859549 CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:862355-863554 [ Homo sapiens (human) ]

Gene ID: 126859549, updated on 12-Sep-2024

Summary

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Gene symbol
LOC126859549
Gene description
CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:862355-863554
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 includes enhancers that were validated by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay. The major subregion had activity 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. Three subregions were also shown to be active enhancers by ChIP-STARR-seq in primed human embryonic stem cells, where all three are marked by the H3K27ac histone modification and one is additionally marked by H3K4me1. [provided by RefSeq, Oct 2022]
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Genomic context

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See LOC126859549 in Genome Data Viewer
Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (861903..863984)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (720318..724437)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (861903..863984)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene exocyst complex component 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23857 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23858 Neighboring gene MARK2 pseudogene 18 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:692466-693352 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:694782-695290 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:701331-701850 Neighboring gene MPRA-validated peak5620 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16818 Neighboring gene uncharacterized LOC105374873 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancers GRCh37_chr6:829333-829880 and GRCh37_chr6:829881-830426 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:839153-839702 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:867961-868143 Neighboring gene uncharacterized LOC101927691 Neighboring gene uncharacterized LOC124901236

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 hESC enhancer GRCh37_chr6:862597-863290
  • H3K27ac hESC enhancer GRCh37_chr6:863291-863984
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:861903-862596

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_084050.2 

    Range
    101..2182
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    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    861903..863984
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    720318..724437
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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