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LOC130004993 ATAC-STARR-seq lymphoblastoid silent region 2962 [ Homo sapiens (human) ]

Gene ID: 130004993, updated on 14-Oct-2023

Summary

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Gene symbol
LOC130004993
Gene description
ATAC-STARR-seq lymphoblastoid silent region 2962
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 LOC130004993 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 (132421332..132421391)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (133369605..133369664)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902526 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:134208622-134209145 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:134209146-134209668 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2958 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2959 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2960 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:134211239-134211761 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:134211762-134212284 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:134214271-134215047 Neighboring gene PWWP domain containing 2B Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:134218733-134219360 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:134221245-134221872 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:134221873-134222500 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:134222501-134223127 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:134227291-134227958 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:134231824-134232727 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:134232728-134233632 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2961 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2963 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:134235443-134236346 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:134237164-134237690 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:134244072-134244572 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

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_184438.1 

    Range
    101..160
    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
    132421332..132421391
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    133369605..133369664
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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