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LOC130061939 ATAC-STARR-seq lymphoblastoid silent region 9127 [ Homo sapiens (human) ]

Gene ID: 130061939, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130061939
Gene description
ATAC-STARR-seq lymphoblastoid silent region 9127
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 LOC130061939 in Genome Data Viewer
Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (81487919..81488198)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (82404931..82405210)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (79454945..79455224)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene BAH domain and coiled-coil containing 1 Neighboring gene uncharacterized LOC124904084 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79422900-79423848 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79423849-79424797 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:79438477-79438978 Neighboring gene CRISPRi-validated cis-regulatory element chr17.6006 Neighboring gene long intergenic non-protein coding RNA 1971 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79455547-79456267 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:79456989-79457708 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:79460397-79460898 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:79466919-79467642 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12964 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9128 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9129 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12965 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12966 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9130 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79482073-79482696 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79482697-79483322 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12967 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79483947-79484572 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:79484573-79485196 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9133 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9134 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12969 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12970 Neighboring gene actin gamma 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:79495325-79495851 Neighboring gene fascin actin-bundling protein 2, retinal Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:79495852-79496377

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_197032.1 

    Range
    101..380
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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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    81487919..81488198
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791805.1 Reference GRCh38.p14 PATCHES

    Range
    144124..144403
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    82404931..82405210
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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