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LOC122757934 CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:46190573-46191772 [ Homo sapiens (human) ]

Gene ID: 122757934, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122757934
Gene description
CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:46190573-46191772
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 sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It 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. This sequence was defined as a group 2 enhancer that depends on the BRD2, BRD4, P300/CBP, MED14 and CDK7 cofactors, with strong dependence on CDK7. A subregion was also validated as a functional repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 9:DNaseU, primarily UW DNase, weaker open chromatin sites). [provided by RefSeq, Aug 2022]
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Genomic context

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Location:
2p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (45963434..45964633)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (45968430..45969629)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (46191389..46191683)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15688 Neighboring gene PRKCE antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15689 Neighboring gene protein kinase C epsilon Neighboring gene tRNA-Gln (anticodon TTG) 5-1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15690 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15691 Neighboring gene NANOG hESC enhancer GRCh37_chr2:45959936-45960443 Neighboring gene Sharpr-MPRA regulatory region 1594 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:46013490-46014689 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15692 Neighboring gene Sharpr-MPRA regulatory region 10855 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:46050503-46051025 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:46051026-46051547 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15693 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15694 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr2:46063209-46063734 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15695 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11443 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15696 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:46121150-46121322 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15697 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11445 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15698 Neighboring gene uncharacterized LOC124907761 Neighboring gene Sharpr-MPRA regulatory region 2946 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:46185885-46186435 Neighboring gene NANOG hESC enhancer GRCh37_chr2:46200583-46201132 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15699 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:46234481-46235680 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:46242352-46242990 Neighboring gene ribosomal protein L26 pseudogene 15 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:46294453-46295652 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:46344077-46345276 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_58540 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:46371061-46371560 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:46395156-46395343 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:46398401-46398983 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:46406387-46406887 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:46456039-46457023 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15700 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15701 Neighboring gene uncharacterized LOC101926974 Neighboring gene uncharacterized LOC105374581 Neighboring gene ribosomal protein L36a pseudogene 14

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. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, 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

  • Sharpr-MPRA regulatory region 14433

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_076926.2 

    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
    45963434..45964633
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    45968430..45969629
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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