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LOC130060384 ATAC-STARR-seq lymphoblastoid active region 11802 [ Homo sapiens (human) ]

Gene ID: 130060384, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130060384
Gene description
ATAC-STARR-seq lymphoblastoid active region 11802
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 LOC130060384 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 (17628624..17628783)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (17575228..17575387)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (17531938..17532097)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene phosphatidylethanolamine N-methyltransferase Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17494467-17495208 Neighboring gene RNA, U6 small nuclear 468, pseudogene Neighboring gene eukaryotic translation elongation factor 1 alpha 1 pseudogene 43 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17506274-17506774 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:17516315-17516931 Neighboring gene Sharpr-MPRA regulatory region 11476 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17525146-17526020 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17526021-17526896 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17529033-17529938 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17529939-17530844 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11803 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11804 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17570789-17571290 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17571291-17571790 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17578718-17579346 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17584813-17585414 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8249 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17596270-17596984 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17596985-17597697 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8250 Neighboring gene uncharacterized LOC124903943 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17602043-17602561 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17602562-17603079 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17603559-17604070 Neighboring gene Smith-Magenis syndrome chromosome region, candidate 2 Neighboring gene Sharpr-MPRA regulatory region 3199 Neighboring gene Sharpr-MPRA regulatory region 10129 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11805 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11806 Neighboring gene retinoic acid induced 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17620721-17621465

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_195717.1 

    Range
    101..260
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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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    17628624..17628783
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    17575228..17575387
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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