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LOC126806549 CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:231773167-231774366 [ Homo sapiens (human) ]

Gene ID: 126806549, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126806549
Gene description
CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:231773167-231774366
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 two accessible chromatin subregions that were validated as enhancers based on their 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: 2
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (230908452..230909651)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (231391622..231392821)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:231728341-231728999 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:231729658-231730316 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:231730317-231730973 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:231734265-231734922 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:231734923-231735580 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17250 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17251 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12417 Neighboring gene integral membrane protein 2C Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:231742513-231743287 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17253 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:231757691-231758270 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:231758271-231758850 Neighboring gene GPR55 cis regulatory suppressor of immune response RNA Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12418 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12419 Neighboring gene G protein-coupled receptor 55 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:231789302-231790090 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17259 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12420 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12421 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:231804174-231804714 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:231804715-231805254 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17260 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17261 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17262 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17263 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17264 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17265 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17266 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17267 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12422 Neighboring gene COX20 pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17268 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17269 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17270 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17271 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17272 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:231850196-231850380 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17273 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:231851885-231852384 Neighboring gene SPATA3 antisense RNA 1 (head to head) Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:231860347-231860880

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 17255
  • ATAC-STARR-seq lymphoblastoid active region 17256

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_082869.1 

    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    230908452..230909651
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    231391622..231392821
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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