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LOC130056842 ATAC-STARR-seq lymphoblastoid silent region 6330 [ Homo sapiens (human) ]

Gene ID: 130056842, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130056842
Gene description
ATAC-STARR-seq lymphoblastoid silent region 6330
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 LOC130056842 in Genome Data Viewer
Location:
chromosome: 15
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (40368300..40368379)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (38175162..38175241)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (40660501..40660580)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 6286 Neighboring gene RNA, 5S ribosomal pseudogene 392 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:40628805-40629323 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:40632233-40633036 Neighboring gene coiled-coil domain containing 9B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:40635981-40636480 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:40636664-40637261 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:40637262-40637858 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:40646605-40647130 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6328 Neighboring gene uncharacterized LOC124903472 Neighboring gene proline, histidine and glycine rich 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:40655530-40656030 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:40656031-40656531 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:40659527-40660418 Neighboring gene dispatched RND transporter family member 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:40673800-40674300 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:40674955-40675478 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:40675479-40676000 Neighboring gene kinetochore localized astrin (SPAG5) binding protein Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9241 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9242 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:40699201-40699700 Neighboring gene isovaleryl-CoA dehydrogenase

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_191263.1 

    Range
    101..180
    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    40368300..40368379
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    38175162..38175241
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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