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LOC126859757 CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:106967140-106968339 [ Homo sapiens (human) ]

Gene ID: 126859757, updated on 12-Sep-2024

Summary

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Gene symbol
LOC126859757
Gene description
CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:106967140-106968339
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 (MPRA) 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. This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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See LOC126859757 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 (106519265..106520464)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (107695754..107696953)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (106967140..106968339)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene crystallin beta-gamma domain containing 1 Neighboring gene uncharacterized LOC105377924 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:106908781-106909430 Neighboring gene uncharacterized LOC101927405 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:106957727-106958332 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:106959060-106960018 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24888 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24889 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17433 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24891 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:107023180-107023700 Neighboring gene MPRA-validated peak6003 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr6:107033226-107033920 Neighboring gene reticulon 4 interacting protein 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:107061294-107061801 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:107062309-107062815 Neighboring gene RNA, U6 small nuclear 527, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24892 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24893 Neighboring gene glutaminyl-tRNA amidotransferase subunit QRSL1 Neighboring gene ribosomal protein L21 pseudogene 65

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. ATAC-STARR-seq reveals transcription factor-bound activators and silencers within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. PMID 35858748, 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

  • ATAC-STARR-seq lymphoblastoid active region 24890

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_084258.1 

    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    106519265..106520464
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    107695754..107696953
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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