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LOC121587596 H3K27ac hESC enhancer GRCh37_chr17:43138457-43139448 [ Homo sapiens (human) ]

Gene ID: 121587596, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121587596
Gene description
H3K27ac hESC enhancer GRCh37_chr17:43138457-43139448
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 (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 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 two accessible chromatin subregions that were validated as enhancers based on their 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]
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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 (45061089..45062080)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (45914961..45915952)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (43138809..43139103)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene basic proline-rich protein-like Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8605 Neighboring gene uncharacterized LOC107987243 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:43074788-43075540 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:43080963-43081726 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:43083016-43083972 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:43085503-43086003 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:43089992-43090778 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12268 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:43096740-43096919 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8607 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12269 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:43112912-43113412 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:43113413-43113913 Neighboring gene dephospho-CoA kinase domain containing Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:43117423-43118057 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr17:43118058-43118692 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:43118693-43119327 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:43120482-43121367 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:43121368-43122252 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:43124492-43125024 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:43125025-43125555 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8608 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:43137465-43138456 Neighboring gene N-myristoyltransferase 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr17:43168092-43168593 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:43175496-43175996 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:43175997-43176497 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12273 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:43180894-43181394 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:43184227-43184728 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:43189298-43190163 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:43190164-43191028 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:43191895-43192759 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:43198136-43198673 Neighboring gene phospholipase C delta 3 Neighboring gene microRNA 6784 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8609 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8610 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12274 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:43220320-43221042 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:43221043-43221764 Neighboring gene acyl-CoA binding domain containing 4

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 12271
  • ATAC-STARR-seq lymphoblastoid active region 12272
  • Sharpr-MPRA regulatory region 28

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_074981.2 

    Range
    101..1092
    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
    45061089..45062080
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    45914961..45915952
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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