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LOC130063401 ATAC-STARR-seq lymphoblastoid silent region 10003 [ Homo sapiens (human) ]

Gene ID: 130063401, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130063401
Gene description
ATAC-STARR-seq lymphoblastoid silent region 10003
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 LOC130063401 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 (7926050..7926319)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (7927004..7927273)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (7990935..7991204)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:7980702-7981202 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9996 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:7981823-7982699 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:7982700-7983575 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:7984251-7984750 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10000 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10001 Neighboring gene transforming growth factor beta receptor 3 like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:7986451-7987053 Neighboring gene uncharacterized LOC124904629 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10002 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:7991701-7992450 Neighboring gene small nuclear RNA activating complex polypeptide 2 Neighboring gene Sharpr-MPRA regulatory region 3551 Neighboring gene cortexin 1 Neighboring gene translocase of inner mitochondrial membrane 44 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:8007572-8008115 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:8008116-8008658 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:8008659-8009202 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:8009203-8009745 Neighboring gene MPRA-validated peak3325 silencer Neighboring gene ELAV like RNA binding protein 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:8033572-8034184 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:8034185-8034798 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13904 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13905 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:8042669-8043169 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:8066604-8067215 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:8067216-8067826 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10006 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10007 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10008

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_197818.1 

    Range
    101..370
    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
    7926050..7926319
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    7927004..7927273
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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