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LOC130067212 ATAC-STARR-seq lymphoblastoid silent region 13611 [ Homo sapiens (human) ]

Gene ID: 130067212, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130067212
Gene description
ATAC-STARR-seq lymphoblastoid silent region 13611
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 LOC130067212 in Genome Data Viewer
Location:
chromosome: 22
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (30397261..30397330)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (30860591..30860660)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (30793250..30793319)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene coiled-coil domain containing 157 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30766725-30767224 Neighboring gene KIAA1656 protein Neighboring gene ring finger protein 215 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13610 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18837 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13612 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30797780-30798280 Neighboring gene SEC14 like lipid binding 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30798281-30798781 Neighboring gene Sharpr-MPRA regulatory region 13809 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:30817842-30818421 Neighboring gene RNA, U6 small nuclear 564, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13613 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:30822016-30822574 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30822575-30823134 Neighboring gene mitochondrial fission process 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_201627.1 

    Range
    101..170
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    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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    30397261..30397330
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    30860591..30860660
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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