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LOC130060424 ATAC-STARR-seq lymphoblastoid silent region 8271 [ Homo sapiens (human) ]

Gene ID: 130060424, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130060424
Gene description
ATAC-STARR-seq lymphoblastoid silent region 8271
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 LOC130060424 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 (18225927..18226096)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (18172726..18172895)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (18129241..18129410)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene myosin XVA Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:18056260-18056783 Neighboring gene uncharacterized LOC105371567 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8266 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11827 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11828 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:18070429-18070930 Neighboring gene Sharpr-MPRA regulatory region 12190 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11829 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11830 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:18087137-18087974 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8269 Neighboring gene alkB homolog 5, RNA demethylase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11831 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8270 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:18133833-18134668 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:18134669-18135502 Neighboring gene LLGL scribble cell polarity complex component 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:18150319-18150870 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:18151421-18151970 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:18160018-18160684 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11833 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:18161423-18161924 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11834 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:18164285-18164905 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:18164906-18165525 Neighboring gene FLII actin remodeling protein Neighboring gene mitochondrial elongation factor 2

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_194800.1 

    Range
    101..270
    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
    18225927..18226096
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    18172726..18172895
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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