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LOC130062127 ATAC-STARR-seq lymphoblastoid active region 13058 [ Homo sapiens (human) ]

Gene ID: 130062127, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130062127
Gene description
ATAC-STARR-seq lymphoblastoid active region 13058
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 LOC130062127 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 (5980325..5980414)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (6140412..6140501)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (5980324..5980413)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene MIR3976 host gene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9264 Neighboring gene microRNA 3976 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9265 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:5891299-5891826 Neighboring gene uncharacterized LOC121725015 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr18:5899993-5901192 Neighboring gene transmembrane protein 200C Neighboring gene OCT4 hESC enhancer GRCh37_chr18:5941844-5942352 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:5964119-5964619 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr18:5964978-5965478 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13057 Neighboring gene L3MBTL histone methyl-lysine binding protein 4 Neighboring gene RNA, U5F small nuclear 3, pseudogene Neighboring gene Sharpr-MPRA regulatory region 6254 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:6146293-6146793 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13059 Neighboring gene L3MBTL4 antisense RNA 1

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_197194.1 

    Range
    101..190
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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_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    5980325..5980414
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    6140412..6140501
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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