U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC121366035 H3K27ac-H3K4me1 hESC enhancers GRCh37_chr9:139736293-139737174 and GRCh37_chr9:139737175-139738055 [ Homo sapiens (human) ]

Gene ID: 121366035, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC121366035
Gene description
H3K27ac-H3K4me1 hESC enhancers GRCh37_chr9:139736293-139737174 and GRCh37_chr9:139737175-139738055
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. Two adjacent subregions were validated as enhancers by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in primed human embryonic stem cells, where they are marked by the H3K27ac and H3K4me1 histone modifications. Another subregion was validated as an 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 non-DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Activating DNase matched - State 25:Art, potential CNV or repetitive artifacts). This locus also includes two accessible chromatin subregions, one of which was validated as an enhancer and the other as a silencer based on their ability to activate or 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, Jun 2023]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
9q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (136841841..136843603)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (149076043..149077805)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (139736749..139737043)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene RAB, member RAS oncogene family like 6 Neighboring gene nucleolin pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139716743-139717631 Neighboring gene microRNA 4292 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139732768-139733649 Neighboring gene Sharpr-MPRA regulatory region 5679 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139738056-139738936 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20549 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20550 Neighboring gene apical junction component 1 homolog Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20551 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20552 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20553 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29329 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20554 Neighboring gene phosphohistidine phosphatase 1 Neighboring gene MAM domain containing 4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139752096-139752733

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 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

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 variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

Go to the top of the page Help

Other Names

  • ATAC-STARR-seq lymphoblastoid active region 29328
  • ATAC-STARR-seq lymphoblastoid silent region 20548
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139736293-139737174
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139737175-139738055
  • Sharpr-MPRA regulatory region 13741

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_074385.3 

    Range
    101..1863
    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    136841841..136843603
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    149076043..149077805
    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