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LOC127829318 H3K27ac hESC enhancer GRCh37_chr15:40733201-40733702 [ Homo sapiens (human) ]

Gene ID: 127829318, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127829318
Gene description
H3K27ac hESC enhancer GRCh37_chr15:40733201-40733702
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 primed human embryonic stem cells, where it is marked by the H3K27ac histone modification. An 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 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, Jun 2023]
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Genomic context

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See LOC127829318 in Genome Data Viewer
Location:
chromosome: 15
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (40440659..40441503)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (38248033..38248877)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (40732858..40733702)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:40674955-40675478 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:40675479-40676000 Neighboring gene kinetochore localized astrin (SPAG5) binding protein Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9241 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9242 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:40699201-40699700 Neighboring gene isovaleryl-CoA dehydrogenase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:40728630-40729168 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:40729169-40729706 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:40731858-40732395 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:40733703-40734202 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6333 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6334 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:40737995-40738496 Neighboring gene bromo adjacent homology domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9243 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9244 Neighboring gene uncharacterized LOC124903473 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:40755909-40756410 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:40756411-40756910 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9245 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6335 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6336 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:40764047-40764950 Neighboring gene carbohydrate sulfotransferase 14

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 silent region 6331
  • ATAC-STARR-seq lymphoblastoid silent region 6332
  • ReSE screen-validated silencer GRCh37_chr15:40732954-40733139

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_130800.2 

    Range
    101..945
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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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    40440659..40441503
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    38248033..38248877
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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