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LOC130063440 ATAC-STARR-seq lymphoblastoid silent region 10033 [ Homo sapiens (human) ]

Gene ID: 130063440, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130063440
Gene description
ATAC-STARR-seq lymphoblastoid silent region 10033
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 LOC130063440 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 (8577404..8577553)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (8564766..8564915)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (8642288..8642437)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:8576283-8577173 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10030 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13918 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:8587561-8588060 Neighboring gene zinc finger protein 414 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10031 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:8590637-8591612 Neighboring gene uncharacterized LOC124904633 Neighboring gene myosin IF Neighboring gene MPRA-validated peak3335 silencer Neighboring gene MPRA-validated peak3337 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13919 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13920 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13922 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13921 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13923 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10032 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:8643658-8643852 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10034 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:8649461-8650040 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr19:8651198-8651775 Neighboring gene ADAM metallopeptidase with thrombospondin type 1 motif 10 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:8656685-8657283 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:8674492-8674914 Neighboring gene Sharpr-MPRA regulatory region 9055 Neighboring gene NFIL3 like basic leucine zipper Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13924

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_197857.1 

    Range
    101..250
    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
    8577404..8577553
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    8564766..8564915
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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