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LOC129937413 ATAC-STARR-seq lymphoblastoid active region 20403 [ Homo sapiens (human) ]

Gene ID: 129937413, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129937413
Gene description
ATAC-STARR-seq lymphoblastoid active region 20403
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 LOC129937413 in Genome Data Viewer
Location:
chromosome: 3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (124771077..124771156)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (127496923..127497002)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (124489924..124490003)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ribosomal protein S26 pseudogene 22 Neighboring gene microRNA 544b Neighboring gene uridine monophosphate synthetase Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:124469851-124470517 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:124475893-124476862 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:124478413-124479002 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:124479003-124479592 Neighboring gene Sharpr-MPRA regulatory region 9344 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14654 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:124490944-124491659 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:124491660-124492374 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:124493091-124493805 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:124493806-124494521 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:124495953-124496666 Neighboring gene integrin subunit beta 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20404 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20405 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:124509941-124510473 Neighboring gene uncharacterized LOC124909422 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:124531305-124531909 Neighboring gene uncharacterized LOC124906277 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:124545465-124546128 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:124546129-124546792

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_170423.1 

    Range
    101..180
    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    124771077..124771156
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    127496923..127497002
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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