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LOC130001455 ATAC-STARR-seq lymphoblastoid active region 28129 [ Homo sapiens (human) ]

Gene ID: 130001455, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130001455
Gene description
ATAC-STARR-seq lymphoblastoid active region 28129
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 an enhancer based on its ability to activate 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 LOC130001455 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 (1875798..1876077)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (1878303..1878582)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (1875798..1876077)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 3102 Neighboring gene RPS27A pseudogene 14 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:1224129-1224749 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28122 Neighboring gene NANOG hESC enhancer GRCh37_chr9:1273747-1274248 Neighboring gene uncharacterized LOC102723803 Neighboring gene RNA, 5S ribosomal pseudogene 279 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28123 Neighboring gene OCT4 hESC enhancer GRCh37_chr9:1515455-1515956 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28125 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28124 Neighboring gene uncharacterized LOC105375951 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28126 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28127 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:1771313-1771814 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28128 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28130 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28131 Neighboring gene uncharacterized LOC105375952 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:1928727-1929926 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28132 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19729 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19731 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19730 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:2015793-2016349 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19728 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28134 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28133 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:2018973-2019571 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28135 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:2039759-2040308 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28136 Neighboring gene SWI/SNF related BAF chromatin remodeling complex subunit ATPase 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:2135791-2136058 Neighboring gene RNA, U2 small nuclear 25, pseudogene

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_180901.1 

    Range
    101..380
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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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    1875798..1876077
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    1878303..1878582
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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