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LOC130059007 ATAC-STARR-seq lymphoblastoid silent region 7489 [ Homo sapiens (human) ]

Gene ID: 130059007, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130059007
Gene description
ATAC-STARR-seq lymphoblastoid silent region 7489
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 LOC130059007 in Genome Data Viewer
Location:
chromosome: 16
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (50693326..50693835)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (56490960..56491469)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (50727237..50727746)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene NKD inhibitor of WNT signaling pathway 1 Neighboring gene uncharacterized LOC124903773 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:50636563-50637271 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:50640404-50641180 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr16:50643815-50644780 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:50654230-50654780 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:50654831-50655338 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:50658527-50659292 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:50659293-50660056 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10819 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:50677347-50677501 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:50680473-50680991 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:50688285-50688465 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:50699127-50699628 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10820 Neighboring gene uncharacterized LOC101927272 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10821 Neighboring gene sorting nexin 20 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10822 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10823 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10824 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10825 Neighboring gene Sharpr-MPRA regulatory region 14141 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7490 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:50743936-50744141 Neighboring gene nucleotide binding oligomerization domain containing 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10826 Neighboring gene Sharpr-MPRA regulatory region 1297 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10827 Neighboring gene CYLD antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7491 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10828 Neighboring gene microRNA 3181 Neighboring gene CYLD lysine 63 deubiquitinase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7492 Neighboring gene CYLD antisense RNA 2

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_193428.1 

    Range
    101..610
    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    50693326..50693835
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    56490960..56491469
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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