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LOC130059946 ATAC-STARR-seq lymphoblastoid active region 11489 [ Homo sapiens (human) ]

Gene ID: 130059946, updated on 14-Oct-2023

Summary

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Gene symbol
LOC130059946
Gene description
ATAC-STARR-seq lymphoblastoid active region 11489
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 LOC130059946 in Genome Data Viewer
Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (2267007..2267296)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (2154237..2154526)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene SMG6 nonsense mediated mRNA decay factor Neighboring gene RNA, 7SL, cytoplasmic 624, pseudogene Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:2116692-2117891 Neighboring gene heart enhancer 8 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7987 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11479 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:2122139-2123075 Neighboring gene uncharacterized LOC101927839 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11480 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11481 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11482 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11483 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11484 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11485 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11486 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11487 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11488 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:2205337-2206151 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:2206481-2207207 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 16 Neighboring gene serine racemase Neighboring gene small nucleolar RNA, C/D box 91B Neighboring gene TSR1 ribosome maturation factor

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 across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. 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

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_194367.1 

    Range
    101..390
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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
    2267007..2267296
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    2154237..2154526
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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