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LOC113687175 H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100224056-100224820 [ Homo sapiens (human) ]

Gene ID: 113687175, updated on 17-Sep-2024

Summary

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Gene symbol
LOC113687175
Gene description
H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100224056-100224820
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 was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in naive human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. 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 non-DNase unmatched - State 10:DNaseD, primarily Duke DNase, candidate regulatory elements in more likely repressive locations) and K562 erythroleukemia cells (group: K562 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). This locus also includes two accessible chromatin subregions that were validated as silencers based on their 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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See LOC113687175 in Genome Data Viewer
Location:
7q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (100626433..100627197)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (101866514..101867278)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (100224056..100224820)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene PCOLCE antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100201095-100201887 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18448 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18449 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26375 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26376 Neighboring gene procollagen C-endopeptidase enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26377 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18450 Neighboring gene motile sperm domain containing 3 Neighboring gene uncharacterized LOC124901709 Neighboring gene uncharacterized LOC124901710 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100224821-100225583 Neighboring gene transferrin receptor 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26378 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18453 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100246946-100247492 Neighboring gene actin like 6B Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100247493-100248037 Neighboring gene uncharacterized LOC105375429

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. Toward a complete human genome sequence. Sanger Center, et al. Genome Res, 1998 Nov. PMID 9847074
  2. 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
  3. 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
  4. 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 18451
  • ATAC-STARR-seq lymphoblastoid silent region 18452
  • Sharpr-MPRA regulatory region 4647

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_062456.2 

    Range
    101..865
    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    100626433..100627197
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    101866514..101867278
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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