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LOC130066751 ATAC-STARR-seq lymphoblastoid silent region 13347 [ Homo sapiens (human) ]

Gene ID: 130066751, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130066751
Gene description
ATAC-STARR-seq lymphoblastoid silent region 13347
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 LOC130066751 in Genome Data Viewer
Location:
chromosome: 21
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (42514193..42514272)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (40903894..40903973)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (43934303..43934382)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18520 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18521 Neighboring gene radial spoke head component 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr21:43912470-43913669 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13344 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13345 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:43919416-43919916 Neighboring gene RSPH1 divergent transcript Neighboring gene solute carrier family 37 member 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:43932366-43933088 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:43933089-43933811 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13348 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18522 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:43940701-43941202 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:43941203-43941702 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18523 Neighboring gene uncharacterized LOC107987299 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18524 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18525 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18526 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18527 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:43960552-43961217 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:43962233-43963163 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:43965367-43965904 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:43965905-43966440 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18528 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:43985802-43986722 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:43991832-43992575 Neighboring gene uncharacterized LOC101928212

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_201167.1 

    Range
    101..180
    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_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    42514193..42514272
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    40903894..40903973
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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