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LOC130003102 ATAC-STARR-seq lymphoblastoid active region 29349 [ Homo sapiens (human) ]

Gene ID: 130003102, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130003102
Gene description
ATAC-STARR-seq lymphoblastoid active region 29349
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 LOC130003102 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 (137274806..137274985)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (149512851..149513030)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (140169258..140169437)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene ciliary microtubule inner protein 2A Neighboring gene STPG3 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140149187-140150134 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140150135-140151082 Neighboring gene sperm-tail PG-rich repeat containing 3 Neighboring gene negative elongation factor complex member B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:140157448-140158007 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:140165697-140166196 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 torsin family 4 member A Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20607 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29350 Neighboring gene 9q34.3 TOR4A distal recombination region 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 NOTCH regulated ankyrin repeat protein

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_182548.1 

    Range
    101..280
    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
    137274806..137274985
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    149512851..149513030
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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