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LOC129996618 ATAC-STARR-seq lymphoblastoid silent region 17280 [ Homo sapiens (human) ]

Gene ID: 129996618, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129996618
Gene description
ATAC-STARR-seq lymphoblastoid silent region 17280
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 LOC129996618 in Genome Data Viewer
Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (52299786..52299855)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (52138528..52138597)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (52164584..52164653)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene solute carrier family 25 member 20 pseudogene 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:52129168-52129587 Neighboring gene minichromosome maintenance complex component 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24670 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24671 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17279 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24672 Neighboring gene uncharacterized LOC124901329 Neighboring gene Sharpr-MPRA regulatory region 10632 Neighboring gene Sharpr-MPRA regulatory region 10484 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24673 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17281 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17282 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24674 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:52190539-52191144 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:52191145-52191751 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_92086 Neighboring gene Sharpr-MPRA regulatory region 5108 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:52217075-52217574 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:52226353-52226538 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17283 Neighboring gene progestin and adipoQ receptor family member 8 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24676 Neighboring gene VISTA enhancer hs2064 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24678

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_176064.1 

    Range
    101..170
    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    52299786..52299855
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    52138528..52138597
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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