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LOC129999951 ATAC-STARR-seq lymphoblastoid silent region 18970 [ Homo sapiens (human) ]

Gene ID: 129999951, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129999951
Gene description
ATAC-STARR-seq lymphoblastoid silent region 18970
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 LOC129999951 in Genome Data Viewer
Location:
chromosome: 8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (19817657..19817786)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (20082679..20082808)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (19675168..19675297)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene chondroitin sulfate N-acetylgalactosaminyltransferase 1 Neighboring gene uncharacterized LOC124901899 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:19536806-19537406 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27058 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr8:19589033-19590232 Neighboring gene uncharacterized LOC107986920 Neighboring gene MPRA-validated peak6932 silencer Neighboring gene MPRA-validated peak6933 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:19670041-19670619 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27059 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27060 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18969 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27061 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27062 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27063 Neighboring gene uncharacterized LOC124901901 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:19713825-19714324 Neighboring gene integrator complex subunit 10 Neighboring gene NANOG hESC enhancer GRCh37_chr8:19717703-19718429 Neighboring gene uncharacterized LOC105379309

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_179397.1 

    Range
    101..230
    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    19817657..19817786
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    20082679..20082808
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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