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LOC129932088 ATAC-STARR-seq lymphoblastoid active region 2220 [ Homo sapiens (human) ]

Gene ID: 129932088, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129932088
Gene description
ATAC-STARR-seq lymphoblastoid active region 2220
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 LOC129932088 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 (183609233..183609382)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (182968515..182968664)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (183578368..183578517)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2214 Neighboring gene SMG7 nonsense mediated mRNA decay factor Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1632 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2215 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:183540266-183540431 Neighboring gene chromosome 18 open reading frame 32 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2216 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2217 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2218 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:183568525-183569024 Neighboring gene Sharpr-MPRA regulatory region 11944 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2219 Neighboring gene neutrophil cytosolic factor 2 Neighboring gene NCF2-ARPC5 intergenic ENCODE-defined enhancer Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:183604114-183604614 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2221 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1635 Neighboring gene Sharpr-MPRA regulatory region 5056 Neighboring gene actin related protein 2/3 complex subunit 5 Neighboring gene apolipoprotein B mRNA editing enzyme catalytic polypeptide like 4 Neighboring gene ral guanine nucleotide dissociation stimulator like 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 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_165128.1 

    Range
    101..250
    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
    183609233..183609382
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    182968515..182968664
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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