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LOC126861668 CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:124988989-124990188 [ Homo sapiens (human) ]

Gene ID: 126861668, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126861668
Gene description
CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:124988989-124990188
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 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. A subregion was also validated as an enhancer by ChIP-STARR-seq in naive and primed human embryonic stem cells, where it associates with the NANOG transcription factor and is marked by the H3K4me1 histone modification. [provided by RefSeq, Dec 2022]
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Genomic context

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Location:
chromosome: 12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (124504443..124505642)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (124509806..124511005)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:124828658-124829158 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:124829159-124829659 Neighboring gene Sharpr-MPRA regulatory region 3491 Neighboring gene nuclear receptor corepressor 2 Neighboring gene microRNA 6880 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:124853631-124854132 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:124866136-124866684 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:124866685-124867231 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:124868677-124869413 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:124869414-124870149 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:124870150-124870886 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:124870887-124871621 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5057 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7284 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:124876499-124877188 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:124879259-124879948 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:124879949-124880636 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:124883733-124884232 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:124887188-124887832 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:124887833-124888476 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:124897369-124897997 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:124896741-124897368 Neighboring gene Sharpr-MPRA regulatory region 11802 Neighboring gene uncharacterized LOC124903044 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:124911835-124912374 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:124912375-124912913 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:124917115-124917722 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:124917723-124918330 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7285 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:124924007-124924726 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:124924727-124925447 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:124937508-124938346 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5058 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5059 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:124947144-124947710 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:124947711-124948278 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5060 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7287 Neighboring gene conserved acetylation island sequence 32 enhancer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:124963398-124963907 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:124964417-124964926 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:124964927-124965434 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7288 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7289 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:124975405-124975905 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:124979536-124980495 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:124980496-124981454 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:124992013-124992598 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:124992911-124993125 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:124993187-124993772 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:124996849-124997397 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:124997398-124997946 Neighboring gene uncharacterized LOC105370047 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:125005559-125006111 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:125012056-125013044 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:125016945-125017877 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:125024060-125024769 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:125026984-125027517 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:125028586-125029120 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7292 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:125035807-125036625 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:125040245-125041002 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:125042521-125043280 Neighboring gene Sharpr-MPRA regulatory region 1212 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5062 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5061 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5063 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5064 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5065 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7293 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:125052750-125053610 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:125053611-125054471 Neighboring gene Sharpr-MPRA regulatory region 12812 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:125077891-125078394 Neighboring gene uncharacterized LOC101927436

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

General gene information

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Other Names

  • NANOG-H3K4me1 hESC enhancer GRCh37_chr12:124989075-124989662

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_086166.1 

    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    124504443..124505642
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    124509806..124511005
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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