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LOC127884271 H3K4me1 hESC enhancer GRCh37_chr16:67189519-67190420 [ Homo sapiens (human) ]

Gene ID: 127884271, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127884271
Gene description
H3K4me1 hESC enhancer GRCh37_chr16:67189519-67190420
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 was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in naive human embryonic stem cells, where it is marked by the H3K4me1 histone modification. This locus also includes an accessible chromatin subregion that was validated as a silencer based on its 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 LOC127884271 in Genome Data Viewer
Location:
chromosome: 16
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (67155616..67156517)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (72949908..72950809)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (67189519..67190420)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7576 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7577 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7578 Neighboring gene core-binding factor subunit beta Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:67142676-67143418 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:67143419-67144160 Neighboring gene phagophore assembly factor 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7580 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7581 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7582 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10952 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7584 Neighboring gene UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 9 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7585 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:67195788-67196300 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:67196374-67197322 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:67197323-67198271 Neighboring gene Sharpr-MPRA regulatory region 11796 Neighboring gene TNFRSF1A associated via death domain Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10954 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10955 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7588 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:67206328-67206491 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:67207408-67208330 Neighboring gene F-box and leucine rich repeat protein 8 Neighboring gene heat shock transcription factor 4 Neighboring gene microtubule associated tyrosine carboxypeptidase 1 Neighboring gene nucleolar protein 3

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. 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
  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 Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 7583

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_134051.1 

    Range
    101..1002
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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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    67155616..67156517
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    72949908..72950809
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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