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LOC129934175 ATAC-STARR-seq lymphoblastoid active region 16096 [ Homo sapiens (human) ]

Gene ID: 129934175, updated on 14-Oct-2023

Summary

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Gene symbol
LOC129934175
Gene description
ATAC-STARR-seq lymphoblastoid active region 16096
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 LOC129934175 in Genome Data Viewer
Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (80687601..80687690)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (80687850..80687939)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene catenin alpha 2 Neighboring gene uncharacterized LOC107985904 Neighboring gene NANOG hESC enhancer GRCh37_chr2:80557197-80557699 Neighboring gene uncharacterized LOC105374824 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:80591811-80592596 Neighboring gene NANOG hESC enhancer GRCh37_chr2:80592898-80593415 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:80688730-80689234 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:80689235-80689740 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:80709895-80710095 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11685 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16095 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16097 Neighboring gene NANOG hESC enhancer GRCh37_chr2:81005685-81006186 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:81101296-81102149 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:81103634-81104173 Neighboring gene uncharacterized LOC105374827 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:81147049-81147550 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:81420933-81421434 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:81421435-81421934 Neighboring gene ANKRD11 pseudogene 1

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_167199.1 

    Range
    101..190
    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    80687601..80687690
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    80687850..80687939
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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