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LOC130063134 ATAC-STARR-seq lymphoblastoid silent region 9838 [ Homo sapiens (human) ]

Gene ID: 130063134, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130063134
Gene description
ATAC-STARR-seq lymphoblastoid silent region 9838
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 LOC130063134 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 (3360343..3360392)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (3338477..3338526)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (3360341..3360390)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9832 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3189343-3189846 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3189847-3190350 Neighboring gene nicalin Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9833 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3227850-3228390 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3228391-3228930 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3229472-3230011 Neighboring gene CUGBP Elav-like family member 5 Neighboring gene MPRA-validated peak3244 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9834 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9835 Neighboring gene uncharacterized LOC105372244 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:3301113-3301307 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9836 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9837 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13732 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9839 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9840 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9842 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9841 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9843 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13733 Neighboring gene skeletal muscle cis-regulatory module in NFIC intron Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3389688-3390265 Neighboring gene nuclear factor I C Neighboring gene Sharpr-MPRA regulatory region 10296 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3434103-3434880 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3434881-3435658 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3445307-3445848 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9844 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3462537-3463072 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3463073-3463608 Neighboring gene MPRA-validated peak3246 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3465190-3465690 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3465691-3466191 Neighboring gene Sharpr-MPRA regulatory region 13615 Neighboring gene uncharacterized LOC105372246 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3483217-3483755 Neighboring gene small integral membrane protein 24 Neighboring gene small integral membrane protein 44

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_197551.1 

    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    3360343..3360392
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    3338477..3338526
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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