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LOC130067915 ATAC-STARR-seq lymphoblastoid silent region 20649 [ Homo sapiens (human) ]

Gene ID: 130067915, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130067915
Gene description
ATAC-STARR-seq lymphoblastoid silent region 20649
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 LOC130067915 in Genome Data Viewer
Location:
chromosome: X
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (7147673..7148392)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (6701458..6702177)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (7065714..7066433)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene pseudouridine 5'-phosphatase Neighboring gene uncharacterized LOC107987331 Neighboring gene RPS27A pseudogene 17 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:6975911-6976411 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29382 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:6986912-6987412 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:7000180-7000680 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:7000681-7001181 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29383 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29384 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29385 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29386 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29387 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:7033895-7034396 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:7034397-7034896 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29389 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29390 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29391 Neighboring gene microRNA 4767 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:7154725-7155349 Neighboring gene Sharpr-MPRA regulatory region 5189 Neighboring gene steroid sulfatase Neighboring gene NANOG hESC enhancer GRCh37_chrX:7208639-7209140 Neighboring gene MED14-independent group 3 enhancer GRCh37_chrX:7290864-7292063 Neighboring gene NANOG hESC enhancer GRCh37_chrX:7366971-7367514 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:7510918-7511520 Neighboring gene uncharacterized LOC124905241 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:7682068-7682794 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:7682795-7683521 Neighboring gene variable charge X-linked

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_202330.1 

    Range
    101..820
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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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    7147673..7148392
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    6701458..6702177
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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