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LOC113839506 NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr9:128003252-128003756 and GRCh37_chr9:128003757-128004261 [ Homo sapiens (human) ]

Gene ID: 113839506, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113839506
Gene description
NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr9:128003252-128003756 and GRCh37_chr9:128003757-128004261
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 were validated as active enhancers by ChIP-STARR-seq in human embryonic stem cells, where both are associated with the NANOG transcription factor and are marked by the H3K27ac and H3K4me1 histone modifications. 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 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 1:Tss). 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]
Annotation information
Note: This locus has been reviewed for its involvement in coronavirus biology, and is regulatory element in the vicinity of coronavirus related gene(s).
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Genomic context

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Location:
9q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (125240973..125241982)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (137439291..137440299)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (128003649..128003943)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376271 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20275 Neighboring gene Rab9 effector protein with kelch motifs Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29000 Neighboring gene Sharpr-MPRA regulatory region 12295 Neighboring gene HSPA5 divergent transcript Neighboring gene heat shock protein family A (Hsp70) member 5 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:128020420-128020678 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:128024002-128024183 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:128029981-128030481 Neighboring gene ribosomal protein S10 pseudogene 17 Neighboring gene GTPase activating protein and VPS9 domains 1 Neighboring gene RNA, U6 small nuclear 1020, pseudogene

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. 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

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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

  • ATAC-STARR-seq lymphoblastoid active region 29001
  • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:128003252-128003756
  • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:128003757-128004261
  • Sharpr-MPRA regulatory region 7891

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_063123.2 

    Range
    101..1110
    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
    125240973..125241982
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    137439291..137440299
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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