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LOC130063373 ATAC-STARR-seq lymphoblastoid silent region 9983 [ Homo sapiens (human) ]

Gene ID: 130063373, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130063373
Gene description
ATAC-STARR-seq lymphoblastoid silent region 9983
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 LOC130063373 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 (7488892..7489221)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (7489559..7489888)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (7553778..7554107)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene insulin receptor Neighboring gene uncharacterized LOC124904626 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:7212577-7213123 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr19:7213124-7213669 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13874 Neighboring gene MPRA-validated peak3317 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:7257400-7258262 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:7288463-7288964 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:7292867-7293625 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9973 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9974 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9975 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9976 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9977 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13875 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13876 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13877 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13878 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13879 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9978 Neighboring gene Rho/Rac guanine nucleotide exchange factor 18 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:7438718-7439322 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:7439323-7439927 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13880 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:7447849-7448349 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13881 Neighboring gene ARHGEF18 antisense RNA 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:7459704-7460144 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13882 Neighboring gene MPRA-validated peak3319 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:7462888-7463393 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:7463394-7463898 Neighboring gene MPRA-validated peak3320 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9980 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13883 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13884 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13885 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13886 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:7501123-7501310 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr19:7515146-7515690 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr19:7515691-7516233 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9981 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:7541732-7542367 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:7548591-7549112 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9982 Neighboring gene Sharpr-MPRA regulatory region 6634 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9984 Neighboring gene Sharpr-MPRA regulatory region 11228 Neighboring gene peroxisomal biogenesis factor 11 gamma Neighboring gene uncharacterized LOC105372261 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9985 Neighboring gene stabilizer of axonemal microtubules 5 Neighboring gene zinc finger protein 358

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 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_197790.1 

    Range
    101..430
    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
    7488892..7489221
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    7489559..7489888
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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