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LOC124625903 CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:12111509-12112708 [ Homo sapiens (human) ]

Gene ID: 124625903, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124625903
Gene description
CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:12111509-12112708
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. A subregion 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. An overlapping 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 21:Repr, strong Polycomb repression). [provided by RefSeq, Aug 2022]
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Genomic context

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See LOC124625903 in Genome Data Viewer
Location:
12p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (11958315..11959774)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (11827459..11828917)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902877 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5965 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5966 Neighboring gene long intergenic non-protein coding RNA 1252 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5967 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:11744935-11745672 Neighboring gene Sharpr-MPRA regulatory region 654 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:11761757-11762318 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:11762319-11762880 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr12:11762881-11763442 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5968 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4245 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4244 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4243 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4242 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5969 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5970 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5971 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:11819261-11819894 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:11819895-11820529 Neighboring gene uncharacterized LOC124902879 Neighboring gene ETS variant transcription factor 6 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5972 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5973 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5974 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5976 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5975 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5977 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4246 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5978 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5979 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5980 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5981 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5982 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5983 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5984 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5985 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5986 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5987 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5988 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5989 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5990 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5991 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5992 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5993 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:11947826-11948514 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:11948515-11949203 Neighboring gene Sharpr-MPRA regulatory region 735 Neighboring gene Sharpr-MPRA regulatory region 6497 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5994 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5995 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5996 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4247 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5997 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:11991350-11992549 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:12008095-12008671 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:12022641-12023141 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4248 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:12031171-12031968 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:12037195-12038394 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:12038421-12039131 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5998 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:12080535-12080690 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:12102758-12103542 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5999 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:12162287-12163167 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:12161406-12162286 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:12163168-12164048 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6003 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6004 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6005 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4249 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6006 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6007 Neighboring gene Sharpr-MPRA regulatory region 1566 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6008 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:12199831-12200330 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr12:12210407-12211072 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr12:12211073-12211736 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:12216444-12216992 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:12222531-12222710 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6009 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:12225917-12226604 Neighboring gene Sharpr-MPRA regulatory region 14349 Neighboring gene Sharpr-MPRA regulatory region 8243 Neighboring gene BCL2 like 14 Neighboring gene microRNA 1244-4 Neighboring gene prothymosin alpha pseudogene 9

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

General gene information

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Other Names

  • Sharpr-MPRA regulatory region 8951

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_079585.2 

    Range
    101..1560
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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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    11958315..11959774
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    11827459..11828917
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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