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LOC130060770 ATAC-STARR-seq lymphoblastoid silent region 8463 [ Homo sapiens (human) ]

Gene ID: 130060770, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130060770
Gene description
ATAC-STARR-seq lymphoblastoid silent region 8463
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 LOC130060770 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 (39730214..39730773)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (40593774..40594333)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (37886467..37887026)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene VISTA enhancer hs1769 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:37835782-37836282 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12103 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr17:37845149-37846109 Neighboring gene post-GPI attachment to proteins phospholipase 3 Neighboring gene Sharpr-MPRA regulatory region 353 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:37857299-37857800 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:37857801-37858300 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:37861047-37861919 Neighboring gene erb-b2 receptor tyrosine kinase 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:37882556-37883528 Neighboring gene microRNA 4728 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:37896451-37897048 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:37897647-37898244 Neighboring gene migration and invasion enhancer 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8465 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8464 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8466 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12104 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12105 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12106 Neighboring gene growth factor receptor bound protein 7 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12107 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8467 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12108 Neighboring gene IKAROS family zinc finger 3 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:37934634-37934867 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:37940879-37941109 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12109 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12110 Neighboring gene MPRA-validated peak2840 silencer Neighboring gene MPRA-validated peak2841 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:37991649-37992148 Neighboring gene keratin 8 pseudogene 34

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_196032.1 

    Range
    101..660
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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
    39730214..39730773
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    40593774..40594333
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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