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LOC130003984 ATAC-STARR-seq lymphoblastoid silent region 2433 [ Homo sapiens (human) ]

Gene ID: 130003984, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130003984
Gene description
ATAC-STARR-seq lymphoblastoid silent region 2433
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 LOC130003984 in Genome Data Viewer
Location:
chromosome: 10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (69409204..69409303)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (70277247..70277346)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (71168960..71169059)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101928994 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16994 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16995 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3487 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3488 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr10:70991590-70992789 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:71007828-71008366 Neighboring gene hexokinase domain containing 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:71016306-71016498 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:71050933-71051433 Neighboring gene hexokinase 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:71072583-71073084 Neighboring gene ribosomal protein S15a pseudogene 28 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3489 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2430 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3490 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:71080772-71081688 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:71085561-71086169 Neighboring gene Sharpr-MPRA regulatory regions 12566 and 14132 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr10:71088623-71089424 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:71089425-71090226 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:71094713-71095639 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:71096837-71097524 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:71097525-71098210 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:71098899-71099584 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:71103173-71104026 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2431 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:71125753-71126258 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:71126259-71126762 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:71136088-71136610 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:71136611-71137131 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:71149651-71150373 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:71150445-71151156 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2432 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:71176444-71177178 Neighboring gene Sharpr-MPRA regulatory region 2430 Neighboring gene tachykinin receptor 2 Neighboring gene ATP synthase membrane subunit c locus 1 pseudogene 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:71207805-71208306 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:71209624-71210242 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:71210243-71210860 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2434 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:71211741-71212241 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3492 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3493 Neighboring gene tetraspanin 15 Neighboring gene Sharpr-MPRA regulatory region 14270 Neighboring gene MPRA-validated peak1006 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2435 Neighboring gene transmembrane protein 256 pseudogene 1

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_183430.1 

    Range
    101..200
    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    69409204..69409303
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    70277247..70277346
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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