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LOC126805650 CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:20706555-20707754 [ Homo sapiens (human) ]

Gene ID: 126805650, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126805650
Gene description
CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:20706555-20707754
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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Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (20380062..20381261)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (20203665..20204864)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376828 Neighboring gene NANOG hESC enhancer GRCh37_chr1:20605144-20605685 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:20616749-20617260 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:20617261-20617771 Neighboring gene von Willebrand factor A domain containing 5B1 Neighboring gene uncharacterized LOC124903870 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:20669041-20669541 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:20680030-20680530 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:20680531-20681031 Neighboring gene long intergenic non-protein coding RNA 1141 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:20701977-20702476 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 320 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:20727039-20727539 Neighboring gene NANOG hESC enhancer GRCh37_chr1:20729171-20729710 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:20732635-20733223 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:20737119-20737312 Neighboring gene MPRA-validated peak103 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 364 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:20769432-20769932 Neighboring gene uncharacterized LOC124903871 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:20810004-20810938 Neighboring gene calcium/calmodulin dependent protein kinase II inhibitor 1

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 across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. 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

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 321

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_081974.1 

    Range
    101..1300
    Download
    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    20380062..20381261
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    20203665..20204864
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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