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LOC129999634 ATAC-STARR-seq lymphoblastoid silent region 18805 [ Homo sapiens (human) ]

Gene ID: 129999634, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129999634
Gene description
ATAC-STARR-seq lymphoblastoid silent region 18805
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 LOC129999634 in Genome Data Viewer
Location:
chromosome: 7
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (151226982..151227041)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (152400098..152400157)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (150924068..150924127)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150893037-150893776 Neighboring gene IQ motif containing with AAA domain 1 like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150895718-150896704 Neighboring gene ABCF2-H2BK1 readthrough Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:150910975-150912174 Neighboring gene H2B.K variant histone 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:150916273-150916470 Neighboring gene ATP binding cassette subfamily F member 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26853 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26854 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26855 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18806 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150930441-150931006 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150932437-150932937 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:150936637-150937836 Neighboring gene uncharacterized LOC124901779 Neighboring gene chondroitin polymerizing factor 2 Neighboring gene SWI/SNF related BAF chromatin remodeling complex subunit D3 Neighboring gene microRNA 671

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_179080.1 

    Range
    101..160
    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    151226982..151227041
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    152400098..152400157
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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