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LOC130059218 ATAC-STARR-seq lymphoblastoid silent region 7611 [ Homo sapiens (human) ]

Gene ID: 130059218, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130059218
Gene description
ATAC-STARR-seq lymphoblastoid silent region 7611
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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See LOC130059218 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 (67537294..67537573)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (73332061..73332340)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (67571197..67571476)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene ATP6V0D1 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10967 Neighboring gene agouti related neuropeptide Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10968 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:67548235-67548422 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7607 Neighboring gene uncharacterized LOC100505942 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10969 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10970 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10971 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10972 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10973 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7609 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7608 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7610 Neighboring gene RHO family interacting cell polarization regulator 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:67571987-67572608 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10975 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7613 Neighboring gene Sharpr-MPRA regulatory region 14438 Neighboring gene uncharacterized LOC124903703 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:67586099-67586600 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:67586601-67587100 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10977 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10978 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:67596785-67597647 Neighboring gene CTCF divergent transcript Neighboring gene CCCTC-binding factor

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

See Variation Viewer (GRCh37.p13)

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_193639.1 

    Range
    101..380
    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    67537294..67537573
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    73332061..73332340
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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