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LOC130059798 ATAC-STARR-seq lymphoblastoid silent region 7897 [ Homo sapiens (human) ]

Gene ID: 130059798, updated on 14-Oct-2023

Summary

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Gene symbol
LOC130059798
Gene description
ATAC-STARR-seq lymphoblastoid silent region 7897
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 LOC130059798 in Genome Data Viewer
Location:
chromosome: 16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (89247156..89247905)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (95327487..95328236)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 4154 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11397 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:89284467-89284997 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:89284998-89285527 Neighboring gene ZNF778 divergent transcript Neighboring gene Sharpr-MPRA regulatory region 2584 Neighboring gene zinc finger protein 778 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7896 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:89308033-89308549 Neighboring gene uncharacterized LOC124903766 Neighboring gene ankyrin repeat domain containing 11 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:89357571-89358417 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:89360111-89360956 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:89360957-89361803 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:89361804-89362649 Neighboring gene uncharacterized LOC105371414 Neighboring gene keratin-associated protein 5-2-like Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:89372939-89373605 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:89379263-89380057 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:89381655-89382246 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:89382247-89382838 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:89383431-89384022 Neighboring gene uncharacterized LOC128462377 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:89384023-89384614 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:89385876-89386388 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:89386389-89386902 Neighboring gene uncharacterized LOC100287036 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7898 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:89389210-89390409

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 across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. 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

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_194219.1 

    Range
    101..850
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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
    89247156..89247905
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    95327487..95328236
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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