U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC127816478 H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:136038755-136039477 [ Homo sapiens (human) ]

Gene ID: 127816478, updated on 12-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC127816478
Gene description
H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:136038755-136039477
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 region includes an enhancer that was validated by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in primed human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. This locus also includes an accessible chromatin subregion that was validated as a silencer based on its ability to 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, May 2023]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See LOC127816478 in Genome Data Viewer
Location:
chromosome: 9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (133163368..133164109)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (145377465..145378206)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (136038755..136039496)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA U13 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:135976589-135977788 Neighboring gene ral guanine nucleotide dissociation stimulator Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29228 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:135995531-135996227 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20442 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20443 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20444 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20445 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr9:136002206-136003405 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:136008097-136008641 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29229 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29230 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29231 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29232 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29233 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:136019197-136019756 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20446 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20447 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:136024237-136024884 Neighboring gene globoside alpha-1,3-N-acetylgalactosaminyltransferase 1 (FORS blood group) Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:136062831-136063698 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:136075403-136076124 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:136081856-136082043 Neighboring gene odorant binding protein 2B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:136102720-136103675 Neighboring gene lipocalin 1 pseudogene 1

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. 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
  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 Variation Viewer (GRCh37.p13)

General gene information

Go to the top of the page Help

Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 20450

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_117970.2 

    Range
    101..842
    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    133163368..133164109
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    145377465..145378206
    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