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LOC126861620 P300/CBP strongly-dependent group 1 enhancer GRCh37_chr12:104680011-104681210 [ Homo sapiens (human) ]

Gene ID: 126861620, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126861620
Gene description
P300/CBP strongly-dependent group 1 enhancer GRCh37_chr12:104680011-104681210
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). The major subregion had activity in HCT116 colorectal carcinoma cells, where it was defined as a group 1 enhancer that depends on the BRD2, BRD4, P300/CBP, MED14 and CDK7 cofactors, with strong dependence on P300/CBP. Two subregions were also shown to be active enhancers by ChIP-STARR-seq in primed human embryonic stem cells, where both are associated with the NANOG transcription factor and are marked by the H3K27ac and H3K4me1 histone modifications. 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. Another subregion containing a Neanderthal adaptively introgressed genetic variant was also validated as an enhancer by MPRAs in K562 erythroleukemia cells, with activity observed for both the introgressed and non-introgressed 12:104680661 variant alleles. [provided by RefSeq, Sep 2023]
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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 (104286233..104287818)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (104247931..104249516)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23757 Neighboring gene long intergenic non-protein coding RNA 2385 Neighboring gene Sharpr-MPRA regulatory region 15351 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23771 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:104609333-104609949 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:104609950-104610565 Neighboring gene NFE2L2 motif-containing MPRA enhancer 194 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23775 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23777 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:104628245-104628471 Neighboring gene thioredoxin reductase 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23786 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23788 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23792 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23801 Neighboring gene uncharacterized LOC124903002 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23817 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:104665873-104667072 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23822 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23828 Neighboring gene ribosomal protein L18a pseudogene 3 Neighboring gene Sharpr-MPRA regulatory region 5029 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:104681597-104682144 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:104682145-104682690 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23836 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23840 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:104697445-104698317 Neighboring gene EP300 interacting inhibitor of differentiation 3 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23854 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:104736854-104737098 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23864 Neighboring gene Sharpr-MPRA regulatory region 7710 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:104761070-104761775 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:104765060-104765816 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:104765817-104766574 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:104766575-104767330 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:104768893-104769404 Neighboring gene uncharacterized LOC105369949 Neighboring gene MPRA-validated peak1927 silencer

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 6906
  • ATAC-STARR-seq lymphoblastoid active region 6907
  • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:104680503-104681050
  • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:104681051-104681596
  • Neanderthal introgressed variant-containing enhancer experimental_23834

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_086118.2 

    Range
    101..1686
    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
    104286233..104287818
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    104247931..104249516
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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