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LOC130059238 ATAC-STARR-seq lymphoblastoid silent region 7626 [ Homo sapiens (human) ]

Gene ID: 130059238, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130059238
Gene description
ATAC-STARR-seq lymphoblastoid silent region 7626
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 LOC130059238 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 (67806999..67807118)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (73602022..73602141)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (67840902..67841021)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:67710969-67711925 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:67711926-67712881 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:67717419-67718618 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10980 Neighboring gene Gfo/Idh/MocA-like oxidoreductase domain containing 2 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr16:67743233-67744011 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:67744012-67744789 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10981 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7623 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7624 Neighboring gene RAN binding protein 10 Neighboring gene Sharpr-MPRA regulatory region 12647 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10982 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10983 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10984 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:67839586-67840206 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:67840207-67840826 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:67851021-67851203 Neighboring gene translin associated factor X interacting protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:67859393-67860253 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10986 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10987 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10988 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7627 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:67876439-67877185 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10990 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7628 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7629 Neighboring gene centromere protein T Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10991 Neighboring gene THAP domain containing 11 Neighboring gene nuclear transport factor 2

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_193659.1 

    Range
    101..220
    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
    67806999..67807118
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    73602022..73602141
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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