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LOC129998903 ATAC-STARR-seq lymphoblastoid silent region 18417 [ Homo sapiens (human) ]

Gene ID: 129998903, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129998903
Gene description
ATAC-STARR-seq lymphoblastoid silent region 18417
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 LOC129998903 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 (100127397..100127876)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (101367248..101367727)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (99725020..99725499)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene minichromosome maintenance complex component 7 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18415 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:99698720-99699272 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26336 Neighboring gene adaptor related protein complex 4 subunit mu 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:99704970-99705470 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:99708249-99708476 Neighboring gene TATA-box binding protein associated factor 6 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26337 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26338 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26339 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:99723160-99723829 Neighboring gene canopy FGF signaling regulator 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26340 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18416 Neighboring gene metallo-beta-lactamase domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26341 Neighboring gene ribosomal protein L7 pseudogene 60 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:99745544-99746156 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26342 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26343 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:99746769-99747381 Neighboring gene late endosomal/lysosomal adaptor, MAPK and MTOR activator 4

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_178348.1 

    Range
    101..580
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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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    100127397..100127876
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    101367248..101367727
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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