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LOC130059553 ATAC-STARR-seq lymphoblastoid silent region 7767 [ Homo sapiens (human) ]

Gene ID: 130059553, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130059553
Gene description
ATAC-STARR-seq lymphoblastoid silent region 7767
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 LOC130059553 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 (83802233..83802392)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (89867963..89868122)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (83835838..83835997)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene cadherin 13 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr16:83761543-83762043 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11231 Neighboring gene uncharacterized LOC124903810 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:83841377-83841878 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:83846533-83847044 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:83847045-83847556 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:83847557-83848068 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:83850559-83851758 Neighboring gene CDH13 antisense oligodendrocyte and neuron associated lncRNA Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:83873977-83874624 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:83875273-83875919 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:83874625-83875272 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:83879897-83880398 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:83880399-83880898 Neighboring gene CDH13 antisense RNA 2 Neighboring gene MPRA-validated peak2652 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr16:83912211-83912369 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7769 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7770 Neighboring gene NANOG hESC enhancer GRCh37_chr16:83942352-83942873 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:83945234-83946433 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:83947165-83947672 Neighboring gene uncharacterized LOC105371372 Neighboring gene heat shock factor binding protein 1 Neighboring gene malonyl-CoA decarboxylase

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_193974.1 

    Range
    101..260
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    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
    83802233..83802392
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    89867963..89868122
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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