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LOC129936817 ATAC-STARR-seq lymphoblastoid active region 19918 [ Homo sapiens (human) ]

Gene ID: 129936817, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129936817
Gene description
ATAC-STARR-seq lymphoblastoid active region 19918
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 LOC129936817 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 (51390759..51390808)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (51421176..51421225)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (51428190..51428239)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene dedicator of cytokinesis 3 Neighboring gene NANOG hESC enhancer GRCh37_chr3:50928312-50928861 Neighboring gene Sharpr-MPRA regulatory region 894 Neighboring gene ST13, Hsp70 interacting protein pseudogene 14 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14407 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:51263456-51264655 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19916 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:51377300-51378184 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19917 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14408 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14409 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14410 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14411 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:51430225-51430730 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:51430731-51431238 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14412 Neighboring gene RNA binding motif protein 15B Neighboring gene DDB1 and CUL4 associated factor 1 Neighboring gene mesencephalic astrocyte derived neurotrophic factor Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19919 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14413 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14414 Neighboring gene uncharacterized LOC105377085 Neighboring gene Sharpr-MPRA regulatory region 10823

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_169828.1 

    Range
    101..150
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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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    51390759..51390808
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    51421176..51421225
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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