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LOC130057514 ATAC-STARR-seq lymphoblastoid silent region 6645 [ Homo sapiens (human) ]

Gene ID: 130057514, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130057514
Gene description
ATAC-STARR-seq lymphoblastoid silent region 6645
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 LOC130057514 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 (74322738..74322857)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (72190491..72190610)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (74615079..74615198)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene coiled-coil domain containing 33 Neighboring gene uncharacterized LOC105370893 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:74524367-74525566 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74526358-74526954 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74531317-74531912 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74531913-74532508 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74536295-74536796 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74537297-74538296 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74555642-74556474 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74556475-74557305 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74569034-74569758 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74569759-74570483 Neighboring gene VISTA enhancer hs2614 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74593043-74593864 Neighboring gene uncharacterized LOC124903525 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9747 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:74611467-74612377 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74620529-74621030 Neighboring gene cytochrome P450 family 11 subfamily A member 1 Neighboring gene uncharacterized LOC124903524 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6646 Neighboring gene CYP11A1 promoter region Neighboring gene peptidylprolyl isomerase A pseudogene 46

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_191935.1 

    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    74322738..74322857
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_021160016.1 Reference GRCh38.p14 PATCHES

    Range
    152007..152126
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    72190491..72190610
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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