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LOC126859889 CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:166671501-166672700 [ Homo sapiens (human) ]

Gene ID: 126859889, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126859889
Gene description
CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:166671501-166672700
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. In HCT116 colorectal carcinoma cells, a subregion was defined as a group 2 enhancer that depends on the BRD2, BRD4, P300/CBP, MED14 and CDK7 cofactors, with strong dependence on CDK7. Another subregion was also validated as an enhancer by ChIP-STARR-seq in naive human embryonic stem cells, where it is marked by the H3K4me1 histone modification. [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC126859889 in Genome Data Viewer
Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (166258013..166259292)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (167627861..167629140)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 153, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr6:166637642-166637828 Neighboring gene uncharacterized LOC101929297 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:166654823-166655322 Neighboring gene G protein subunit gamma 5 pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:166666701-166667359 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:166667360-166668017 Neighboring gene uncharacterized LOC107986668 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:166685531-166686036 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:166688619-166689118 Neighboring gene uncharacterized LOC105378118 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25429 Neighboring gene uncharacterized LOC107986669 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17774 Neighboring gene proline rich 18

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

General gene information

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Other Names

  • H3K4me1 hESC enhancer GRCh37_chr6:166671913-166672780

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_084390.2 

    Range
    101..1380
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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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    166258013..166259292
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_187557.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    37434..38713
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    167627861..167629140
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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