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LOC130001358 ATAC-STARR-seq lymphoblastoid silent region 19648 [ Homo sapiens (human) ]

Gene ID: 130001358, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130001358
Gene description
ATAC-STARR-seq lymphoblastoid silent region 19648
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 LOC130001358 in Genome Data Viewer
Location:
chromosome: 8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (143990508..143990647)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (145150706..145150845)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (145064676..145064815)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:144939917-144940418 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:144940419-144940918 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144948081-144948772 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:144949483-144950125 Neighboring gene epiplakin 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19626 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144953345-144953987 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144959005-144959528 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144959529-144960052 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144964657-144965548 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144965549-144966440 Neighboring gene Sharpr-MPRA regulatory region 5026 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:144977006-144977576 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:144990280-144990475 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144999476-145000347 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28075 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:145002644-145002773 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28076 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:145006382-145007317 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19628 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19629 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28077 Neighboring gene plectin Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19630 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28078 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19631 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28079 Neighboring gene Sharpr-MPRA regulatory region 8265 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19632 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19633 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28080 Neighboring gene uncharacterized LOC124902040 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19634 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:145020877-145021664 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:145021665-145022452 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:145024027-145024814 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19635 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28081 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19636 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19637 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19638 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19639 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:145031501-145032404 Neighboring gene microRNA 661 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:145038963-145039740 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:145039741-145040518 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:145040519-145041295 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:145046021-145046870 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:145046871-145047718 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19641 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19642 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19643 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:145050844-145051005 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:145051354-145051848 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19646 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28082 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28083 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:145060401-145061304 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19647 Neighboring gene Sharpr-MPRA regulatory region 3935 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:145065969-145066470 Neighboring gene poly(ADP-ribose) polymerase family member 10 Neighboring gene glutamate ionotropic receptor NMDA type subunit associated protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28085 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19651 Neighboring gene spermatogenesis and centriole associated 1 Neighboring gene NANOG hESC enhancer GRCh37_chr8:145092262-145092784 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:145103171-145104068 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19652 Neighboring gene sphingomyelin phosphodiesterase 5 (pseudogene)

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_180804.1 

    Range
    101..240
    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    143990508..143990647
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    145150706..145150845
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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