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LOC127266766 H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:967845-968714 [ Homo sapiens (human) ]

Gene ID: 127266766, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127266766
Gene description
H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:967845-968714
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 human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. 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 three 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 LOC127266766 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (1032465..1033557)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (462601..463693)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (967845..968937)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ribosomal protein L39 pseudogene 12 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:948847-949738 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:949739-950630 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:950916-951136 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18 Neighboring gene ISG15 ubiquitin like modifier Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:956772-957971 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:959156-960132 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:960133-961108 Neighboring gene agrin Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:965235-966104 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 22 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:974926-975604 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 23 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 24 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:989815-989997 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:994105-994948 Neighboring gene uncharacterized LOC100288175 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:995794-996637 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:997280-997780 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 26 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1000356-1000856 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1000857-1001357 Neighboring gene uncharacterized LOC105378948 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 27 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 28 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:1004678-1005443 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1009379-1009878 Neighboring gene ring finger protein 223

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 19
  • ATAC-STARR-seq lymphoblastoid silent region 20
  • ATAC-STARR-seq lymphoblastoid silent region 21
  • ReSE screen-validated silencer GRCh37_chr1:968588-968708

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_088641.2 

    Range
    101..1193
    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    1032465..1033557
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    462601..463693
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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