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LOC130060438 ATAC-STARR-seq lymphoblastoid active region 11846 [ Homo sapiens (human) ]

Gene ID: 130060438, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130060438
Gene description
ATAC-STARR-seq lymphoblastoid active region 11846
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 LOC130060438 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 (18933565..18933764)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (18880080..18880279)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (18836878..18837077)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene coiled-coil domain-containing protein 144A-like Neighboring gene RNA, 7SL, cytoplasmic 627, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11840 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:18759295-18759795 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:18761223-18761795 Neighboring gene phosphoribosyl pyrophosphate synthetase associated protein 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11843 Neighboring gene RAN binding protein 1 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11844 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11845 Neighboring gene small nucleolar RNA MBII-202 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:18850561-18851174 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:18851175-18851788 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8281 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:18864393-18865390 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:18866439-18866973 Neighboring gene solute carrier family 5 member 10 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:18866974-18867507 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:18871247-18872190 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:18874077-18875018 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:18883844-18884799 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:18884800-18885754 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:18885755-18886709 Neighboring gene family with sequence similarity 83 member G Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8282

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_195755.1 

    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    18933565..18933764
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    18880080..18880279
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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