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LOC130062089 ATAC-STARR-seq lymphoblastoid active region 13028 [ Homo sapiens (human) ]

Gene ID: 130062089, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130062089
Gene description
ATAC-STARR-seq lymphoblastoid active region 13028
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 LOC130062089 in Genome Data Viewer
Location:
chromosome: 18
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (2907585..2907784)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (3063087..3063286)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (2907583..2907782)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr18:2653904-2654533 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9246 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9247 Neighboring gene Sharpr-MPRA regulatory region 12050 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13027 Neighboring gene CBX3 pseudogene 2 Neighboring gene structural maintenance of chromosomes flexible hinge domain containing 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:2716737-2717237 Neighboring gene uncharacterized LOC124904372 Neighboring gene Sharpr-MPRA regulatory region 3375 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9248 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9249 Neighboring gene Sharpr-MPRA regulatory region 4434 Neighboring gene elastin microfibril interfacer 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9250 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:2919273-2920004 Neighboring gene lipin 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13029 Neighboring gene CHORDC1 pseudogene 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13030 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13031 Neighboring gene uncharacterized LOC105371963

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_197162.1 

    Range
    101..300
    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_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    2907585..2907784
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    3063087..3063286
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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