U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC124629402 H3K4me1 hESC enhancer GRCh37_chr12:70273005-70273542 [ Homo sapiens (human) ]

Gene ID: 124629402, updated on 12-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC124629402
Gene description
H3K4me1 hESC enhancer GRCh37_chr12:70273005-70273542
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 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 ChIP-STARR-seq massively parallel reporter assay (MPRA) in naive human embryonic stem cells, where it is marked by the H3K4me1 histone modification. A subregion was also validated as a repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Repressive DNase unmatched - State 8:EnhW, candidate weak enhancer and open chromatin). 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]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See LOC124629402 in Genome Data Viewer
Location:
12q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (69879225..69879762)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (69858381..69858918)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (70273005..70273542)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105369823 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:70082106-70083305 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:70083432-70084000 Neighboring gene bestrophin 3 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:70087234-70087434 Neighboring gene uncharacterized LOC101928002 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4654 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:70153303-70153894 Neighboring gene RAB3A interacting protein Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_30842 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_30867 Neighboring gene myelin regulatory factor like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:70272467-70273004 Neighboring gene MPRA-validated peak1788 silencer Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr12:70289930-70290500 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr12:70290501-70291069 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6656 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:70325891-70326586 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:70332766-70333393 Neighboring gene MPRA-validated peak1789 silencer Neighboring gene MPRA-validated peak1793 silencer Neighboring gene MPRA-validated peak1794 silencer Neighboring gene uncharacterized LOC124902959 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:70463098-70463693 Neighboring gene OCT4 hESC enhancer GRCh37_chr12:70484701-70485202 Neighboring gene MPRA-validated peak1795 silencer Neighboring gene histone PARylation factor 1 pseudogene

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

Related articles in PubMed

  1. 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
  2. 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
  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

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See Variation Viewer (GRCh37.p13)

General gene information

Go to the top of the page Help

Other Names

  • ATAC-STARR-seq lymphoblastoid active region 6655
  • Sharpr-MPRA regulatory region 6106

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_079763.2 

    Range
    101..638
    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    69879225..69879762
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    69858381..69858918
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases