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LOC130060019 ATAC-STARR-seq lymphoblastoid silent region 8034 [ Homo sapiens (human) ]

Gene ID: 130060019, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130060019
Gene description
ATAC-STARR-seq lymphoblastoid silent region 8034
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 LOC130060019 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 (4358891..4358940)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (4248154..4248203)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (4262186..4262235)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904156 Neighboring gene ubiquitin conjugating enzyme E2 G1 Neighboring gene major facilitator superfamily domain containing 1 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4220485-4221252 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4236451-4237364 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4240300-4241080 Neighboring gene Sharpr-MPRA regulatory region 13848 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11538 Neighboring gene RNA, 7SL, cytoplasmic 774, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11539 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:4286079-4286578 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8037 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:4298989-4299759 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:4299760-4300529 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4315987-4316488 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8038 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:4337297-4337951 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4342684-4343184 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4351479-4351979 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4353153-4353653 Neighboring gene SPNS lysolipid transporter 3, sphingosine-1-phosphate (putative) Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4379777-4380645 Neighboring gene uncharacterized LOC124903899 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4384268-4385023 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11541

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_194440.1 

    Range
    101..150
    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    4358891..4358940
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    4248154..4248203
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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