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LOC126862553 CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:37618166-37619365 [ Homo sapiens (human) ]

Gene ID: 126862553, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126862553
Gene description
CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:37618166-37619365
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 (MPRA). In HCT116 colorectal carcinoma cells, a subregion was defined as a group 2 enhancer that depends on the BRD2, BRD4, P300/CBP, MED14 and CDK7 cofactors, with strong dependence on CDK7. Another subregion was also validated as an enhancer by ChIP-STARR-seq in naive human embryonic stem cells, where it associates with the NANOG transcription factor and is marked by the H3K27ac and H3K4me1 histone modifications. This locus also includes three 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: 17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (39461263..39463112)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (40325169..40327018)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene F-box and leucine rich repeat protein 20 Neighboring gene microRNA 548BC Neighboring gene MPRA-validated peak2834 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:37489325-37489835 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:37493495-37494252 Neighboring gene Sharpr-MPRA regulatory region 12086 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:37557132-37557424 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8453 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8454 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8455 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8456 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:37558864-37559028 Neighboring gene mediator complex subunit 1 Neighboring gene U6 spliceosomal RNA Neighboring gene cyclin dependent kinase 12 Neighboring gene RNA, U6 small nuclear 233, 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. 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
  3. 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

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 12094
  • ATAC-STARR-seq lymphoblastoid active region 12095
  • ATAC-STARR-seq lymphoblastoid active region 12096
  • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:37617516-37618440

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_087050.2 

    Range
    101..1950
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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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    39461263..39463112
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    40325169..40327018
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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