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LOC130060083 ATAC-STARR-seq lymphoblastoid active region 11582 [ Homo sapiens (human) ]

Gene ID: 130060083, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130060083
Gene description
ATAC-STARR-seq lymphoblastoid active region 11582
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 LOC130060083 in Genome Data Viewer
Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (5785643..5785832)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (5679963..5680152)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (5688963..5689152)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903903 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr17:5623530-5624450 Neighboring gene nipsnap homolog 1 (C. elegans) pseudogene Neighboring gene MED14-independent group 3 enhancer GRCh37_chr17:5635830-5637029 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11583 Neighboring gene uncharacterized LOC339166 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:5740831-5741332 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:5800477-5801376 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:5801377-5802275 Neighboring gene NANOG hESC enhancer GRCh37_chr17:5816130-5816781 Neighboring gene Sharpr-MPRA regulatory region 3217 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:5972935-5973766 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:5983596-5984097 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:5990226-5990917 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:5999248-6000148 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:6000149-6001047 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:6001681-6002448 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:6011648-6011820 Neighboring gene WSC domain containing 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:6038771-6039272 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr17:6042463-6043017 Neighboring gene uncharacterized LOC105371508

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_194504.1 

    Range
    101..290
    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    5785643..5785832
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    5679963..5680152
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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