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LOC126860549 MED14-independent group 3 enhancer GRCh37_chr8:144911577-144912776 [ Homo sapiens (human) ]

Gene ID: 126860549, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126860549
Gene description
MED14-independent group 3 enhancer GRCh37_chr8:144911577-144912776
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 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. Another subregion was also validated as an enhancer by ChIP-STARR-seq in primed 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: 8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (143829033..143830606)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (144985734..144987307)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene IQ motif and ankyrin repeat containing 1 Neighboring gene SREBF pathway regulator in golgi 1 pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144852281-144852954 Neighboring gene scribble planar cell polarity protein Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:144896321-144896985 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:144897270-144897902 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:144897903-144898535 Neighboring gene microRNA 937 Neighboring gene uncharacterized LOC107986985 Neighboring gene poly(U) binding splicing factor 60 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:144918993-144919720 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144923032-144923762 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:144923763-144924492 Neighboring gene nuclear receptor binding protein 2 Neighboring gene microRNA 6845 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:144939917-144940418 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:144940419-144940918 Neighboring gene epiplakin 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144948081-144948772 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:144949483-144950125 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19626 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144953345-144953987

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 19624
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144911557-144912256

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_085049.3 

    Range
    101..1674
    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    143829033..143830606
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    144985734..144987307
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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