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LOC113121301 H3K27ac hESC enhancer GRCh37_chr6:105307475-105307974 [ Homo sapiens (human) ]

Gene ID: 113121301, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113121301
Gene description
H3K27ac hESC enhancer GRCh37_chr6:105307475-105307974
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 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 histone modification. A subregion was also 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 DNase matched - State 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 1:Tss). 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]
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Genomic context

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Location:
6q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (104859348..104860099)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (106035370..106036121)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (105307589..105307883)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377918 Neighboring gene MPRA-validated peak5987 silencer Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:104919911-104920484 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:104937517-104938123 Neighboring gene VISTA enhancer hs1452 Neighboring gene Sharpr-MPRA regulatory region 1651 Neighboring gene MPRA-validated peak5988 silencer Neighboring gene HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1 Neighboring gene RNA, U6 small nuclear 897, pseudogene Neighboring gene poly(A) binding protein cytoplasmic 4 pseudogene Neighboring gene MPRA-validated peak5989 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:105384704-105385204 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:105385205-105385705 Neighboring gene LIN28B antisense RNA 1 Neighboring gene lin-28 homolog B

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 silent region 17425
  • Sharpr-MPRA regulatory region 9880

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_061632.3 

    Range
    101..852
    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    104859348..104860099
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    106035370..106036121
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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