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LOC126859682 CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:45868755-45869954 [ Homo sapiens (human) ]

Gene ID: 126859682, updated on 12-Sep-2024

Summary

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Gene symbol
LOC126859682
Gene description
CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:45868755-45869954
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. Two subregions were also shown to be active enhancers by ChIP-STARR-seq in naive human embryonic stem cells, where one was associated with the OCT4 and NANOG transcription factors and the other was marked by the H3K4me1 histone modification. [provided by RefSeq, Oct 2022]
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Genomic context

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See LOC126859682 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 (45900928..45902765)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (45736215..45738052)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (45868665..45870502)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene RUNX2 antisense RNA 1 Neighboring gene U6 spliceosomal RNA Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:45623433-45624632 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24644 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24645 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24646 Neighboring gene NANOG hESC enhancer GRCh37_chr6:45669242-45669749 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17267 Neighboring gene Sharpr-MPRA regulatory region 1586 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:45722353-45722853 Neighboring gene VISTA enhancer hs1461 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:45866604-45867157 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24647 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:45894464-45895128 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:45895129-45895792 Neighboring gene chloride intracellular channel 5 Neighboring gene uncharacterized LOC124901326 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:45928377-45928876 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24648 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:45982710-45983554 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:45983555-45984399 Neighboring gene RNA, U6 small nuclear 754, pseudogene

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

  • H3K4me1 hESC enhancer GRCh37_chr6:45869658-45870502
  • OCT4-NANOG hESC enhancer GRCh37_chr6:45868665-45869353

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_084183.2 

    Range
    101..1938
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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
    45900928..45902765
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    45736215..45738052
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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