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LOC129934385 ATAC-STARR-seq lymphoblastoid active region 16239 [ Homo sapiens (human) ]

Gene ID: 129934385, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129934385
Gene description
ATAC-STARR-seq lymphoblastoid active region 16239
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 LOC129934385 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 (97645987..97646166)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (98104208..98104387)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (98262450..98262629)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373499 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:98233139-98233656 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:98235127-98236008 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:98238522-98239022 Neighboring gene MPRA-validated peak3795 silencer Neighboring gene UBTF like 6 (pseudogene) Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:98261483-98262417 Neighboring gene cytochrome c oxidase subunit 5B Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:98278969-98279610 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11792 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11793 Neighboring gene actin related protein 1B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16241 Neighboring gene U4 spliceosomal RNA Neighboring gene chromosome 2 open reading frame 92 Neighboring gene RNA, U4 small nuclear 8, pseudogene

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_167403.1 

    Range
    101..280
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    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
    97645987..97646166
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791765.1 Reference GRCh38.p14 PATCHES

    Range
    572018..572197
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    98104208..98104387
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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