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LOC126860989 P300/CBP strongly-dependent group 1 enhancer GRCh37_chr10:88730527-88731726 [ Homo sapiens (human) ]

Gene ID: 126860989, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126860989
Gene description
P300/CBP strongly-dependent group 1 enhancer GRCh37_chr10:88730527-88731726
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 region includes enhancers that were validated by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA). In HCT116 colorectal carcinoma cells, a subregion 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. Another subregion was also validated as an enhancer by ChIP-STARR-seq in naive human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. This locus also includes an accessible chromatin subregion that was validated as a silencer based on its ability to repress 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]
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Genomic context

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Location:
chromosome: 10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (86970182..86971969)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (87853891..87855678)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene bone morphogenetic protein receptor type 1A Neighboring gene RNA, U1 small nuclear 19, pseudogene Neighboring gene Sharpr-MPRA regulatory region 4131 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3698 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88700126-88700626 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:88704401-88704974 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:88713843-88714442 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:88715044-88715643 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:88718646-88719245 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:88720446-88721046 Neighboring gene multimerin 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88721647-88722246 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3700 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3699 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88726172-88726925 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88726926-88727678 Neighboring gene Sharpr-MPRA regulatory region 6517 Neighboring gene uncharacterized LOC124902474 Neighboring gene ADIRF antisense RNA 1 Neighboring gene synuclein gamma Neighboring gene ArfGAP with GTPase domain, ankyrin repeat and PH domain 11 Neighboring gene adipogenesis regulatory factor Neighboring gene MPRA-validated peak1043 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3702 Neighboring gene BMS1 pseudogene 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88779570-88780070 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88780071-88780571 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:88784270-88785122 Neighboring gene family with sequence similarity 25 member A

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 silent region 2575
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:88729939-88730690

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_085488.2 

    Range
    101..1888
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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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    86970182..86971969
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    87853891..87855678
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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