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LOC129998873 ATAC-STARR-seq lymphoblastoid active region 26315 [ Homo sapiens (human) ]

Gene ID: 129998873, updated on 14-Oct-2023

Summary

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Gene symbol
LOC129998873
Gene description
ATAC-STARR-seq lymphoblastoid active region 26315
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 LOC129998873 in Genome Data Viewer
Location:
chromosome: 7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (99438388..99438677)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (100677289..100677578)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901707 Neighboring gene small nucleolar RNA U13 Neighboring gene BUD31 homolog Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18409 Neighboring gene ATP5MF-PTCD1 readthrough Neighboring gene pentatricopeptide repeat domain 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:99020619-99021120 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:99027477-99028073 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:99032915-99033062 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:99034189-99034714 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18410 Neighboring gene SAP domain containing ribonucleoprotein pseudogene Neighboring gene cleavage and polyadenylation specific factor 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:99049670-99050230 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:99053345-99054147 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:99058948-99059448 Neighboring gene ATP synthase membrane subunit f Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:99062959-99063576 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:99063577-99064192

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_178318.1 

    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    99438388..99438677
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    100677289..100677578
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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