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LOC130066965 ATAC-STARR-seq lymphoblastoid silent region 13470 [ Homo sapiens (human) ]

Gene ID: 130066965, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130066965
Gene description
ATAC-STARR-seq lymphoblastoid silent region 13470
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 LOC130066965 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 (19986901..19987340)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (20364528..20364967)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (19974424..19974863)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene thioredoxin reductase 2 Neighboring gene endogenous retrovirus group K member 24 Gag polyprotein-like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19927919-19928489 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:19928490-19929059 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13467 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13468 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13469 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18664 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18665 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:19931341-19931910 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:19931911-19932479 Neighboring gene Sharpr-MPRA regulatory region 10527 Neighboring gene Sharpr-MPRA regulatory region 2516 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19940787-19941410 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19941411-19942032 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:19942297-19942948 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:19943251-19943418 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:19949617-19950332 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:19950333-19951048 Neighboring gene catechol-O-methyltransferase Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:19951049-19951764 Neighboring gene microRNA 4761 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19970318-19971255 Neighboring gene ARVCF delta catenin family member Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19971256-19972192 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19973130-19974065 Neighboring gene uncharacterized LOC124905082 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:19998201-19999025 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13471 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13472 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18666 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18667 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:20018676-20019372 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18668 Neighboring gene transport and golgi organization 2 homolog Neighboring gene microRNA 185

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_201380.1 

    Range
    101..540
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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
    19986901..19987340
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    20364528..20364967
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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