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LOC130002658 ATAC-STARR-seq lymphoblastoid active region 29049 [ Homo sapiens (human) ]

Gene ID: 130002658, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130002658
Gene description
ATAC-STARR-seq lymphoblastoid active region 29049
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 LOC130002658 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 (127777739..127777828)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (139985193..139985282)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (130540018..130540107)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene peptidyl-tRNA hydrolase 1 homolog Neighboring gene cilia and flagella associated protein 157 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:130476687-130477343 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29045 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29046 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29047 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:130478240-130478416 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:130480462-130480664 Neighboring gene tetratricopeptide repeat domain 16 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130488893-130489394 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:130496147-130497053 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20308 Neighboring gene torsin family 2 member A Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130504225-130504852 Neighboring gene SH2 domain containing 3C Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130523547-130524424 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130524425-130525300 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130526508-130527090 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20309 Neighboring gene uncharacterized LOC107987132 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:130539526-130539796 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29050 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:130545551-130545741 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29052 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20310 Neighboring gene Sharpr-MPRA regulatory region 7866 Neighboring gene Sharpr-MPRA regulatory region 2041 Neighboring gene microRNA 3960 Neighboring gene microRNA 2861 Neighboring gene cyclin dependent kinase 9

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_182104.1 

    Range
    101..190
    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
    127777739..127777828
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    139985193..139985282
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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