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LOC112163662 MED14-independent group 3 enhancer GRCh37_chr13:48640162-48641361 [ Homo sapiens (human) ]

Gene ID: 112163662, updated on 10-Dec-2024

Summary

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Gene symbol
LOC112163662
Gene description
MED14-independent group 3 enhancer GRCh37_chr13:48640162-48641361
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 sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as an active enhancer by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) 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. A subregion was also validated as a functional enhancer 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 Activating DNase matched - State 14:Gen5', transcription transition, highly expressed genes towards 5' end). The same subregion also displayed weak activation by Sharpr-MPRA in K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 17:Gen3', transcription 3' end of genes, highly expressed; more exonic). This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its 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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See LOC112163662 in Genome Data Viewer
Location:
13q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (48066026..48067225)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (47286407..47287606)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (48640162..48641361)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5330 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr13:48575750-48576949 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:48577621-48578218 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:48578817-48579414 Neighboring gene SUCLA2 antisense RNA 1 Neighboring gene uncharacterized LOC124903172 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr13:48610990-48611866 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr13:48611867-48612742 Neighboring gene nudix hydrolase 15 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr13:48646101-48647300 Neighboring gene MED4 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 5997 Neighboring gene mediator complex subunit 4 Neighboring gene uncharacterized LOC105370198 Neighboring gene RNA polymerase II subunit K pseudogene 2

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
  3. ATAC-STARR-seq reveals transcription factor-bound activators and silencers within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. PMID 35858748, 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

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 7722
  • Sharpr-MPRA regulatory region 3717

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_056637.2 

    Range
    101..1300
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000013.11 Reference GRCh38.p14 Primary Assembly

    Range
    48066026..48067225
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    47286407..47287606
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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