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LOC130003106 ATAC-STARR-seq lymphoblastoid silent region 20607 [ Homo sapiens (human) ]

Gene ID: 130003106, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130003106
Gene description
ATAC-STARR-seq lymphoblastoid silent region 20607
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 LOC130003106 in Genome Data Viewer
Location:
chromosome: 9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (137286770..137286869)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (149524817..149524916)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (140181222..140181321)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140149187-140150134 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140150135-140151082 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:140157448-140158007 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:140165697-140166196 Neighboring gene negative elongation factor complex member B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29349 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20604 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20605 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20606 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29350 Neighboring gene 9q34.3 TOR4A distal recombination region Neighboring gene torsin family 4 member A Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20608 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:140191021-140191688 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:140193329-140194222 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20609 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20610 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20611 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140196022-140196940 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140201529-140202446 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140204820-140205742 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140205743-140206664 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140209101-140210036 Neighboring gene NOTCH regulated ankyrin repeat protein Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20613 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20614 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140213503-140214138 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140214773-140215407 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140215408-140216041 Neighboring gene exonuclease 3'-5' domain containing 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140245426-140245935 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140245936-140246444 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:140262690-140263291 Neighboring gene MPRA-validated peak7347 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr9:140264677-140264866 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20615 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20616 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:140306223-140306402 Neighboring gene Sharpr-MPRA regulatory region 4638 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140311837-140312663 Neighboring gene uncharacterized LOC124902354

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 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_182552.1 

    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    137286770..137286869
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    149524817..149524916
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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