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LOC129930515 ATAC-STARR-seq lymphoblastoid silent region 868 [ Homo sapiens (human) ]

Gene ID: 129930515, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129930515
Gene description
ATAC-STARR-seq lymphoblastoid silent region 868
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 LOC129930515 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (50977632..50977801)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (50857513..50857682)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (51443304..51443473)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene Fas associated factor 1 Neighboring gene Sharpr-MPRA regulatory region 673 Neighboring gene mitochondrial ribosomal protein S6 pseudogene 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:51375804-51376372 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:51376373-51376941 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:51418325-51418899 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1012 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 864 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 865 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 866 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1013 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 867 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1014 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1015 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1016 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1017 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 869 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 870 Neighboring gene CRISPRi-validated cis-regulatory element chr1.6035 Neighboring gene cyclin dependent kinase inhibitor 2C Neighboring gene microRNA 4421 Neighboring gene microRNA 6500

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_163566.1 

    Range
    101..270
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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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    50977632..50977801
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    50857513..50857682
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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