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LOC127814619 H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:33167185-33167750 [ Homo sapiens (human) ]

Gene ID: 127814619, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127814619
Gene description
H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:33167185-33167750
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 region includes an enhancer that was validated by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in naive and primed human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. An overlapping accessible chromatin subregion was used in a lentiviral ReSE (repressive ability of silencer elements) screen that assays for cell survival based on transcriptional repression of an apoptosis-inducing fusion protein. That subregion was identified as a functional silencer in K562 erythroleukemia cells. This locus also includes two accessible chromatin subregions, one of which was validated as an enhancer and the other as a silencer based on their ability to activate or 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 LOC127814619 in Genome Data Viewer
Location:
chromosome: 9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (33167088..33167769)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (33185721..33186402)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (33167086..33167767)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:33111589-33112188 Neighboring gene beta-1,4-galactosyltransferase 1 Neighboring gene microRNA 12117 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28273 Neighboring gene uncharacterized LOC124902141 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28274 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28275 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28276 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28277 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28278 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28279 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28280 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:33161108-33162102 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:33163497-33163996 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28282 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28283 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:33167751-33168315 Neighboring gene B4GALT1 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:33172776-33173276 Neighboring gene RNA, U4atac small nuclear 15, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28286 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28287 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:33233401-33234600 Neighboring gene serine peptidase inhibitor Kazal type 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. Systematic identification of silencers in human cells. Pang B, et al. Nat Genet, 2020 Mar. PMID 32094911, Free PMC Article
  2. 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
  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 Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 28284
  • ATAC-STARR-seq lymphoblastoid silent region 19832
  • ReSE screen-validated silencer GRCh37_chr9:33167086-33167359

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_116140.3 

    Range
    101..782
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    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    33167088..33167769
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    33185721..33186402
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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