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LOC130060690 ATAC-STARR-seq lymphoblastoid silent region 8427 [ Homo sapiens (human) ]

Gene ID: 130060690, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130060690
Gene description
ATAC-STARR-seq lymphoblastoid silent region 8427
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 LOC130060690 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 (32519280..32519709)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (33465041..33465470)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (30846298..30846727)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:30814538-30815097 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8423 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:30817300-30817421 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12031 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8425 Neighboring gene uncharacterized LOC124903982 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:30824438-30824945 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:30830591-30831361 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:30832133-30832903 Neighboring gene uncharacterized LOC105371734 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12032 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12033 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12034 Neighboring gene uncharacterized LOC107985012 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8426 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:30849483-30850006 Neighboring gene cyclin dependent kinase 5 regulatory subunit 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:30850007-30850529 Neighboring gene myosin ID Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr17:30873137-30873636 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12035 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12036 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:31010379-31011000 Neighboring gene MPRA-validated peak2803 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8428 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8429 Neighboring gene uncharacterized LOC124903981 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12038 Neighboring gene Sharpr-MPRA regulatory region 12414 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12039 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:31203674-31203861 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:31213662-31214258 Neighboring gene CRISPRi-validated MYO1D non-hub enhancer 1 Neighboring gene CRISPRi-validated cis-regulatory element chr17.1747 Neighboring gene Sharpr-MPRA regulatory region 12135 Neighboring gene MYO1D divergent transcript Neighboring gene H2B.N variant histone 1

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 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_195966.1 

    Range
    101..530
    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
    32519280..32519709
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    33465041..33465470
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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