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LOC126859678 CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:43977969-43979168 [ Homo sapiens (human) ]

Gene ID: 126859678, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126859678
Gene description
CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:43977969-43979168
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer
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. An accessible chromatin subregion was used in a lentiviral ReSE (repressive ability of silencer elements) screen that assays for cell survival based on transcriptional repression of an apoptosis-inducing fusion protein. That subregion was identified as a functional silencer in HepG2 liver carcinoma cells. [provided by RefSeq, Jun 2023]
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Genomic context

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See LOC126859678 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 (44010232..44011431)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (43841940..43843139)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene RNA polymerase I and III subunit C Neighboring gene uncharacterized LOC124901321 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:43961654-43962154 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24624 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17244 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:43972319-43972950 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:44007317-44008074 Neighboring gene long intergenic non-protein coding RNA 3040 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:44009776-44010524 Neighboring gene Sharpr-MPRA regulatory region 2143 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24625 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:44019358-44019952 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:44022316-44022816 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24626 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17245 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:44030458-44031420 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17247 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24628 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24627 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17248 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24629 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24630 Neighboring gene stem cell inhibitory RNA transcript Neighboring gene Sharpr-MPRA regulatory region 9341 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91788 Neighboring gene Sharpr-MPRA regulatory region 15428 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:44069931-44070480 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91802 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:44070481-44071029 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91811 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:44075151-44075650 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91827 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91835 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91840 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17250 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17251 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17252 Neighboring gene ribosomal protein L29 pseudogene 16 Neighboring gene mitochondrial ribosomal protein L14 Neighboring gene transmembrane protein 63B

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. Systematic identification of silencers in human cells. Pang B, et al. Nat Genet, 2020 Mar. PMID 32094911, Free PMC Article
  2. Differential cofactor dependencies define distinct types of human enhancers. Neumayr C, et al. Nature, 2022 Jun. PMID 35650434, 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

  • ReSE screen-validated silencer GRCh37_chr6:43978259-43978457

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_084179.1 

    Range
    101..1300
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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
    44010232..44011431
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    43841940..43843139
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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