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LOC129936670 ATAC-STARR-seq lymphoblastoid silent region 14308 [ Homo sapiens (human) ]

Gene ID: 129936670, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129936670
Gene description
ATAC-STARR-seq lymphoblastoid silent region 14308
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 LOC129936670 in Genome Data Viewer
Location:
chromosome: 3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (47299725..47299774)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (47316104..47316153)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (47341215..47341264)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene SET domain containing 2, histone lysine methyltransferase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14306 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14307 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19809 Neighboring gene MPRA-validated peak4632 silencer Neighboring gene KIF9 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:47238926-47239426 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19810 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:47301362-47302268 Neighboring gene small nucleolar RNA, C/D box 13 pseudogene 3 Neighboring gene small nucleolar RNA, C/D box 13J Neighboring gene kinesin family member 9 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:47323613-47324812 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19812 Neighboring gene kelch like family member 18 Neighboring gene Sharpr-MPRA regulatory region 13740 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:47403837-47405036 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:47421897-47422574 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:47422575-47423250 Neighboring gene PTPN23 divergent transcript Neighboring gene ReSE screen-validated silencer GRCh37_chr3:47440022-47440203 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:47446437-47446936 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:47447130-47447995 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:47457269-47457770 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:47457771-47458270 Neighboring gene protein tyrosine phosphatase non-receptor type 23 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19815 Neighboring gene SREBF chaperone Neighboring gene small nucleolar RNA U13

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_169681.1 

    Range
    101..150
    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    47299725..47299774
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    47316104..47316153
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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