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LOC130064329 ATAC-STARR-seq lymphoblastoid silent region 10561 [ Homo sapiens (human) ]

Gene ID: 130064329, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130064329
Gene description
ATAC-STARR-seq lymphoblastoid silent region 10561
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 LOC130064329 in Genome Data Viewer
Location:
chromosome: 19
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (37962255..37962504)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (40764323..40764572)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (38452895..38453144)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372395 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:38353930-38354430 Neighboring gene uncharacterized LOC107985301 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10559 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14557 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14558 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14559 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:38405529-38406394 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:38406395-38407260 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14560 Neighboring gene WD repeat domain 87 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10560 Neighboring gene signal induced proliferation associated 1 like 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:38423536-38424198 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:38453618-38454118 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10562 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14561 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14562 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14563 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:38472499-38473000 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:38479003-38479508 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:38479509-38480014 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:38480015-38480522 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:38480523-38481028 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:38481029-38481534 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr19:38489623-38490822 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:38494121-38494652 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14564 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14565 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:38503265-38503837 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:38515553-38516056 Neighboring gene uncharacterized LOC105372396 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:38516057-38516560 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:38527685-38528186 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14566 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14567 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr19:38538329-38539077 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14568 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:38542997-38543498 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:38546196-38546766 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:38561125-38561626 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:38561627-38562126 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:38565075-38565574 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:38572086-38572639 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:38602551-38603168 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:38609967-38610170 Neighboring gene MPRA-validated peak3469 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:38620740-38621240 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:38621241-38621741 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:38623222-38623722 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:38634171-38635020 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:38648368-38648546 Neighboring gene small nucleolar RNA, C/D box 152

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_198746.1 

    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    37962255..37962504
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    40764323..40764572
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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