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LOC129994089 ATAC-STARR-seq lymphoblastoid silent region 16106 [ Homo sapiens (human) ]

Gene ID: 129994089, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129994089
Gene description
ATAC-STARR-seq lymphoblastoid silent region 16106
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 LOC129994089 in Genome Data Viewer
Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (76715932..76716181)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (77197815..77198064)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (76011757..76012006)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene IQ motif containing GTPase activating protein 2 Neighboring gene Sharpr-MPRA regulatory region 1022 Neighboring gene coagulation factor II thrombin receptor like 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:76013800-76014300 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:76014301-76014801 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16107 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22695 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22696 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22697 Neighboring gene non-protein coding RNA, upstream of F2R/PAR1 Neighboring gene coagulation factor II thrombin receptor Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:76068685-76069184 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:76074968-76075586 Neighboring gene small nucleolar RNA U13 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:76094678-76095178 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:76099560-76100759 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:76101363-76101946 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:76101947-76102528 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:76103693-76104276 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:76110384-76111038 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:76114571-76115188 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:76115189-76115806 Neighboring gene F2R like trypsin receptor 1

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_173535.1 

    Range
    101..350
    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    76715932..76716181
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    77197815..77198064
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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