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LOC129930426 ATAC-STARR-seq lymphoblastoid active region 953 [ Homo sapiens (human) ]

Gene ID: 129930426, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129930426
Gene description
ATAC-STARR-seq lymphoblastoid active region 953
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 LOC129930426 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (44810188..44810277)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (44681342..44681431)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (45275860..45275949)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 818 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:45251699-45252384 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:45252385-45253070 Neighboring gene bestrophin 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:45257343-45258034 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:45258727-45259416 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:45265053-45265721 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 820 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 949 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:45271492-45272342 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:45272786-45273985 Neighboring gene polo like kinase 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:45274044-45274893 Neighboring gene dynein light chain Tctex-type 4 Neighboring gene BTB domain containing 19 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 821 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr1:45284771-45285427 and GRCh37_chr1:45285428-45286084 Neighboring gene uncharacterized LOC107984952 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:45286741-45287398 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:45287399-45288054 Neighboring gene RNA, U5E small nuclear 6, pseudogene Neighboring gene patched 2

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_163478.1 

    Range
    101..190
    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    44810188..44810277
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    44681342..44681431
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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