U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC126861090 CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:129860232-129861431 [ Homo sapiens (human) ]

Gene ID: 126861090, updated on 12-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC126861090
Gene description
CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:129860232-129861431
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 an enhancer that was validated 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]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See LOC126861090 in Genome Data Viewer
Location:
chromosome: 10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (128061968..128063168)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (128960526..128961725)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (129860232..129861432)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr10:129702059-129702280 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2931 Neighboring gene clarin 3 Neighboring gene uncharacterized LOC124902557 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:129733337-129734076 Neighboring gene protein tyrosine phosphatase receptor type E Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:129775634-129776134 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:129820967-129821467 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:129843223-129843724 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:129843725-129844224 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4197 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4198 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:129861772-129862370 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:129867603-129867800 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:129876157-129876658 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:129876659-129877158 Neighboring gene lncRNA antisense to PTPRE protein-coding gene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:129889651-129890152 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:129890153-129890652 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2932 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4201 Neighboring gene marker of proliferation Ki-67 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2933 Neighboring gene NANOG hESC enhancer GRCh37_chr10:129963700-129964282 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr10:129970982-129972181 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr10:130000381-130000888 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr10:129999872-130000380 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:130007752-130008313 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2934 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2935 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2936 Neighboring gene long intergenic non-protein coding RNA 1163 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:130109218-130109718 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:130109719-130110219 Neighboring gene uncharacterized LOC124902558

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

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 within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. PMID 35858748, Free PMC Article

GeneRIFs: Gene References Into Functions

Phenotypes

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

Go to the top of the page Help

Other Names

  • ATAC-STARR-seq lymphoblastoid active region 4199
  • ATAC-STARR-seq lymphoblastoid active region 4200

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_085589.2 

    Range
    101..1301
    Download
    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    128061968..128063168
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    128960526..128961725
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases