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LOC121466692 MED14-independent group 3 enhancer GRCh37_chr12:12592110-12593309 [ Homo sapiens (human) ]

Gene ID: 121466692, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121466692
Gene description
MED14-independent group 3 enhancer GRCh37_chr12:12592110-12593309
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 in HCT116 colorectal carcinoma cells. This sequence 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 both HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin) and K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Aug 2022]
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Genomic context

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See LOC121466692 in Genome Data Viewer
Location:
12p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (12439176..12440375)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (12308334..12309533)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (12592589..12592883)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene MANSC domain containing 1 Neighboring gene ribosomal protein L23a pseudogene 66 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4252 Neighboring gene CRISPRi-validated cis-regulatory element chr12.586 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:12509797-12510475 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6011 Neighboring gene loss of heterozygosity on chromosome 12, region 2 Neighboring gene BLOC-1 related complex subunit 5 Neighboring gene Sharpr-MPRA regulatory region 10643 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:12560630-12560819 Neighboring gene Sharpr-MPRA regulatory region 7135 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_25257 Neighboring gene adaptor related protein complex 3 subunit sigma 1 pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:12610012-12610690 Neighboring gene dual specificity phosphatase 16 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:12686984-12687949 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:12688131-12688632 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4254 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6012 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6013 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4255 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4256 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4257 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4258

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

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

  • Sharpr-MPRA regulatory region 10190

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_074623.2 

    Range
    101..1300
    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
    12439176..12440375
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_011332696.1 Reference GRCh38.p14 PATCHES

    Range
    408179..409378
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    12308334..12309533
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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