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LOC130004998 ATAC-STARR-seq lymphoblastoid silent region 2966 [ Homo sapiens (human) ]

Gene ID: 130004998, updated on 14-Oct-2023

Summary

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Gene symbol
LOC130004998
Gene description
ATAC-STARR-seq lymphoblastoid silent region 2966
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 LOC130004998 in Genome Data Viewer
Location:
chromosome: 10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (132448568..132448637)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (133397227..133397296)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 3068 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:134252266-134252930 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:134252931-134253594 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2964 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2965 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4225 Neighboring gene long intergenic non-protein coding RNA 2870 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:134266794-134267658 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2968 Neighboring gene uncharacterized LOC105378569 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:134278755-134279345 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:134290270-134290870 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:134290871-134291472 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:134293876-134294475 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:134312545-134313046 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:134313047-134313546 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:134318393-134319092 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:134319093-134319792 Neighboring gene uncharacterized LOC107984282 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:134329666-134330173 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:134330174-134330682 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:134330683-134331190 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:134331699-134332206 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:134341290-134341790 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2969

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

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_184443.1 

    Range
    101..170
    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    132448568..132448637
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    133397227..133397296
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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