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LOC130060998 ATAC-STARR-seq lymphoblastoid silent region 8605 [ Homo sapiens (human) ]

Gene ID: 130060998, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130060998
Gene description
ATAC-STARR-seq lymphoblastoid silent region 8605
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 LOC130060998 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 (44970430..44970499)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (45824352..45824421)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (43047798..43047867)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene kinesin family member 18B Neighboring gene microRNA 6783 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12267 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:43025111-43025630 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:43031038-43031303 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:43039086-43039586 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8604 Neighboring gene basic proline-rich protein-like Neighboring gene complement C1q like 1 Neighboring gene uncharacterized LOC107987243 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:43074788-43075540 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:43080963-43081726 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:43083016-43083972 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:43085503-43086003 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:43089992-43090778 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12268 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:43096740-43096919 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8607 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12269 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:43112912-43113412 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:43113413-43113913 Neighboring gene dephospho-CoA kinase domain containing Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:43117423-43118057 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr17:43118058-43118692 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:43118693-43119327 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:43120482-43121367 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:43121368-43122252 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:43124492-43125024 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:43125025-43125555 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8608 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:43137465-43138456 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:43138457-43139448

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_196234.1 

    Range
    101..170
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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
    44970430..44970499
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    45824352..45824421
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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