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LOC129933229 ATAC-STARR-seq lymphoblastoid active region 15402 [ Homo sapiens (human) ]

Gene ID: 129933229, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129933229
Gene description
ATAC-STARR-seq lymphoblastoid active region 15402
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 LOC129933229 in Genome Data Viewer
Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (20675725..20675844)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (20709041..20709160)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (20875485..20875604)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene HCLS1 binding protein 3 Neighboring gene uncharacterized LOC124907740 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15397 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:20840103-20840604 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15398 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15399 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15400 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:20850539-20851276 Neighboring gene uncharacterized LOC105373466 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:20865647-20866477 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11215 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11214 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11213 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15401 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:20869955-20870900 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15403 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15404 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15405 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:20893576-20893760 Neighboring gene growth differentiation factor 7 Neighboring gene lipid droplet associated hydrolase Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:21021737-21022562 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15407 Neighboring gene long intergenic non-protein coding RNA 2850

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_166254.1 

    Range
    101..220
    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    20675725..20675844
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    20709041..20709160
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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