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LOC130060659 ATAC-STARR-seq lymphoblastoid silent region 8411 [ Homo sapiens (human) ]

Gene ID: 130060659, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130060659
Gene description
ATAC-STARR-seq lymphoblastoid silent region 8411
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 LOC130060659 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 (31488470..31488519)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (32433816..32433865)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (29815488..29815537)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene RAB11 family interacting protein 4 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:29751937-29752664 Neighboring gene uncharacterized LOC105371725 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:29760725-29761454 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:29762116-29762616 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:29762617-29763117 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12011 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:29781223-29781724 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:29781725-29782224 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:29784216-29785064 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:29785065-29785912 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:29786467-29786968 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:29786969-29787468 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:29794364-29795058 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr17:29796711-29797212 Neighboring gene RNA, 7SL, cytoplasmic 79, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:29803345-29804161 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8410 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12012 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:29825931-29826892 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:29826893-29827852 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12013 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:29836658-29837448 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:29850121-29850755 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:29851414-29852028 Neighboring gene Sharpr-MPRA regulatory region 11348 Neighboring gene RNA, 7SL, cytoplasmic 45, pseudogene Neighboring gene microRNA 4724

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_195943.1 

    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
    31488470..31488519
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    32433816..32433865
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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