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LOC129995600 ATAC-STARR-seq lymphoblastoid silent region 16824 [ Homo sapiens (human) ]

Gene ID: 129995600, updated on 27-Aug-2024

Summary

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Gene symbol
LOC129995600
Gene description
ATAC-STARR-seq lymphoblastoid silent region 16824
Gene type
biological region
Feature type(s)
regulatory: 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 sequence represents an accessible chromatin region 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) massively parallel reporter assay (MPRA) in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (1609723..1610342)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (1472724..1473343)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986555 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:1576654-1577427 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:1586829-1587011 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:1594421-1594938 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:1596143-1596696 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:1597733-1597967 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16822 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16823 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:1606326-1606826 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:1606827-1607327 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr6:1607685-1608194 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23864 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:1613862-1614479 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:1614480-1615096 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:1618844-1619706 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23865 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:1629302-1630229 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:1630230-1631156 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:1633959-1634459 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:1636810-1637341 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:1644131-1645078 Neighboring gene uncharacterized LOC107986514 Neighboring gene FOXC1 upstream transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23866 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23867 Neighboring gene forkhead box C1 Neighboring gene GDP-mannose 4,6-dehydratase Neighboring gene NANOG hESC enhancer GRCh37_chr6:1729872-1730373 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23868 Neighboring gene uncharacterized LOC124901239

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

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

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_175046.1 

    Range
    101..720
    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    1609723..1610342
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    1472724..1473343
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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