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LOC129998105 ATAC-STARR-seq lymphoblastoid silent region 18020 [ Homo sapiens (human) ]

Gene ID: 129998105, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129998105
Gene description
ATAC-STARR-seq lymphoblastoid silent region 18020
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 LOC129998105 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 (24758464..24758613)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (24896471..24896620)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (24798083..24798232)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 1103, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25743 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:24613275-24613774 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25744 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25746 Neighboring gene NANOG hESC enhancer GRCh37_chr7:24615771-24616272 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25747 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25748 Neighboring gene SUMO2 pseudogene 14 Neighboring gene protein associated with LIN7 2, MAGUK p55 family member Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:24725223-24725819 Neighboring gene Sharpr-MPRA regulatory region 3197 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:24744538-24744707 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:24757299-24757886 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25750 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25749 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25751 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:24764003-24764686 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:24765371-24766054 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:24766055-24766736 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25752 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25753 Neighboring gene Sharpr-MPRA regulatory region 13058 Neighboring gene gasdermin E Neighboring gene translation initiation factor IF-2-like Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18018 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18019 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25754 Neighboring gene Sharpr-MPRA regulatory region 12520 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25756 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25755 Neighboring gene MPRA-validated peak6442 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:24834361-24834866 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:24834867-24835372 Neighboring gene NANOG hESC enhancer GRCh37_chr7:24841903-24842404 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:24865671-24866870 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25757 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25758 Neighboring gene oxysterol binding protein like 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25759 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25760 Neighboring gene small nuclear ribonucleoprotein polypeptide C pseudogene 19 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:24990225-24990724 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25761 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:25010975-25011630 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18021 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18022 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25762 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:25068437-25068938 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:25098668-25099168 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25763 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25764 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25765 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25766 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25767 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:25163804-25164348 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:25164349-25164892 Neighboring gene cytochrome c, somatic

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_177546.1 

    Range
    101..250
    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
    24758464..24758613
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    24896471..24896620
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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