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LOC126863138 MED14-independent group 3 enhancer GRCh37_chr22:36727082-36728281 [ Homo sapiens (human) ]

Gene ID: 126863138, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126863138
Gene description
MED14-independent group 3 enhancer GRCh37_chr22:36727082-36728281
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 3 enhancer that depends on the BRD2, BRD4, P300/CBP and CDK7 cofactors, but it has limited or no dependence on the MED14 core Mediator complex subunit. Two subregions were also shown to be active enhancers by ChIP-STARR-seq in 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 three 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. [provided by RefSeq, May 2023]
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Genomic context

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Location:
chromosome: 22
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (36330908..36332320)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (36791115..36792527)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18920 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:36651041-36651540 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:36654247-36655038 Neighboring gene apolipoprotein L1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:36682442-36682954 Neighboring gene microRNA 6819 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr22:36696002-36697201 Neighboring gene myosin heavy chain 9 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:36723803-36724432 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:36724433-36725062 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18921 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13663 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13664 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:36734293-36734793 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:36738402-36738920 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:36738921-36739438 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:36739775-36740434 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:36749021-36749750 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:36750200-36750700 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:36750701-36751201 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:36753095-36754036 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18925 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18926 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:36758744-36759684 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18927 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18928 Neighboring gene Sharpr-MPRA regulatory region 8689 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18929 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18930 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18931 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:36781171-36781884 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:36781885-36782598 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13665 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13666 Neighboring gene Sharpr-MPRA regulatory region 2056 Neighboring gene MYH9 divergent transcript Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:36805192-36805812 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:36809052-36809552 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13668 Neighboring gene ribosomal protein S15a pseudogene 38

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 18922
  • ATAC-STARR-seq lymphoblastoid active region 18923
  • ATAC-STARR-seq lymphoblastoid active region 18924
  • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:36726953-36727582
  • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:36727583-36728212

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_087634.3 

    Range
    101..1513
    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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    36330908..36332320
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    36791115..36792527
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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