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LOC130061904 ATAC-STARR-seq lymphoblastoid silent region 9106 [ Homo sapiens (human) ]

Gene ID: 130061904, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130061904
Gene description
ATAC-STARR-seq lymphoblastoid silent region 9106
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 LOC130061904 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 (80261590..80261729)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (81161860..81161999)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (78235389..78235528)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene caspase recruitment domain family member 14 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr17:78178385-78179584 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:78183891-78184046 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12929 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9102 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9103 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78195951-78196788 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78196789-78197626 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78200105-78200606 Neighboring gene N-sulfoglucosamine sulfohydrolase Neighboring gene solute carrier family 26 member 11 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78209849-78210638 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78210639-78211426 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:78227308-78228024 Neighboring gene SLC26A11-RNF213 intergenic CAGE-defined mid-level expression enhancer Neighboring gene CRISPRi-validated cis-regulatory element chr17.5742 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9104 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9105 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:78237270-78237826 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12933 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12934 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9107 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78247837-78248435 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78251821-78252439 Neighboring gene ring finger protein 213 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78258533-78259093 Neighboring gene RNF213 antisense RNA 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:78345568-78346767 Neighboring gene MPRA-validated peak3024 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78354122-78354622 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:78359110-78360309 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78369069-78369570 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78371216-78371723 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78371724-78372230 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12935 Neighboring gene microRNA 4730 Neighboring gene endonuclease V

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_197004.1 

    Range
    101..240
    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
    80261590..80261729
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    81161860..81161999
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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