U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC113839568 H3K4me1 hESC enhancers GRCh37_chr9:94660754-94661368 and GRCh37_chr9:94661369-94661982 [ Homo sapiens (human) ]

Gene ID: 113839568, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC113839568
Gene description
H3K4me1 hESC enhancers GRCh37_chr9:94660754-94661368 and GRCh37_chr9:94661369-94661982
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. Two subregions marked by the H3K4me1 histone modification were validated as active enhancers by ChIP-STARR-seq in naive human embryonic stem cells. An overlapping 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 non-DNase unmatched - State 20:ReprD, Polycomb repression with Duke DNase/promoter and conservation enriched) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). [provided by RefSeq, Nov 2022]
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 (91898472..91899700)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (104064886..104066114)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (94661229..94661523)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene microRNA 3910-2 Neighboring gene microRNA 3910-1 Neighboring gene NANOG hESC enhancer GRCh37_chr9:94455452-94456013 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20027 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_109450 Neighboring gene receptor tyrosine kinase like orphan receptor 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:94544427-94544926 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:94561969-94562469 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:94605877-94606451 Neighboring gene uncharacterized LOC124902210 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:94619147-94619806 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:94619807-94620466 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:94647759-94648342 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:94648343-94648926 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:94648927-94649508 Neighboring gene NANOG hESC enhancer GRCh37_chr9:94656806-94657388 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:94667938-94668501 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr9:94670331-94670937 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:94683071-94683911 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr9:94683912-94684752 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:94696982-94697815 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr9:94702261-94702775 Neighboring gene NANOG hESC enhancer GRCh37_chr9:94707493-94707994 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:94711301-94711802 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:94711803-94712302 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20028 Neighboring gene Sharpr-MPRA regulatory region 183 Neighboring gene Sharpr-MPRA regulatory region 9366 Neighboring gene uncharacterized LOC105376148 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_109489 Neighboring gene uncharacterized LOC107987094

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. 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

  • H3K4me1 hESC enhancer GRCh37_chr9:94660754-94661368
  • H3K4me1 hESC enhancer GRCh37_chr9:94661369-94661982
  • Sharpr-MPRA regulatory region 1031

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_063177.2 

    Range
    101..1329
    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
    91898472..91899700
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    104064886..104066114
    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