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LOC112533641 H3K4me1 hESC enhancer GRCh37_chr17:42275147-42276069 [ Homo sapiens (human) ]

Gene ID: 112533641, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112533641
Gene description
H3K4me1 hESC enhancer GRCh37_chr17:42275147-42276069
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. It was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay in primed human embryonic stem cells, where it is marked by the H3K4me1 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 K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). [provided by RefSeq, Jan 2023]
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Genomic context

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Location:
17q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (44197779..44198701)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (45050882..45051804)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (42275629..42275923)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ankyrin repeat and SOCS box containing 16 Neighboring gene ASB16 antisense RNA 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:42263664-42264198 Neighboring gene transmembrane and ubiquitin like domain containing 2 Neighboring gene ataxin 7 like 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:42274223-42275146 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:42276274-42276829 Neighboring gene ATXN7L3 antisense RNA 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:42277555-42278093 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:42278094-42278631 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:42284331-42284831 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr17:42285473-42286672 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8579 Neighboring gene Sharpr-MPRA regulatory region 7848 Neighboring gene upstream binding transcription factor Neighboring gene microRNA 6782 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8581 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8582 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:42296769-42296933 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8584 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8585 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:42299194-42299798 Neighboring gene SHC adaptor protein 1 pseudogene 2

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. 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

  • Sharpr-MPRA regulatory region 8559

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_056912.2 

    Range
    101..1023
    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    44197779..44198701
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    45050882..45051804
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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