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LOC130002088 ATAC-STARR-seq lymphoblastoid silent region 20038 [ Homo sapiens (human) ]

Gene ID: 130002088, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130002088
Gene description
ATAC-STARR-seq lymphoblastoid silent region 20038
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 LOC130002088 in Genome Data Viewer
Location:
chromosome: 9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (93095695..93096444)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (105262366..105263062)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (95857977..95858726)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:95821078-95822058 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:95822059-95823039 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28609 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:95824548-95825115 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28610 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28611 Neighboring gene sushi domain containing 3 Neighboring gene Sharpr-MPRA regulatory region 12079 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:95844809-95845437 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:95852051-95852551 Neighboring gene uncharacterized LOC101927993 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28612 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20037 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20039 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28613 Neighboring gene caspase recruitment domain family member 19 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:95869787-95870287 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28614 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:95875683-95876631 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:95876632-95877579 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:95881665-95882481 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:95882482-95883297 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:95887196-95887360 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:95888965-95889616 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28616 Neighboring gene ninjurin 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:95893060-95893658 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:95893659-95894256 Neighboring gene uncharacterized LOC124902212 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28617 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20040 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20041 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:95897247-95897843 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:95905234-95906106 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:95906107-95906979 Neighboring gene Sharpr-MPRA regulatory region 13679 Neighboring gene uncharacterized LOC124902213

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_181534.1 

    Range
    101..850
    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    93095695..93096444
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    105262366..105263062
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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