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LOC129936721 ATAC-STARR-seq lymphoblastoid active region 19844 [ Homo sapiens (human) ]

Gene ID: 129936721, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129936721
Gene description
ATAC-STARR-seq lymphoblastoid active region 19844
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 LOC129936721 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 (48897803..48897852)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (48926808..48926857)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (48935236..48935285)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene protein kinase cAMP-dependent type II regulatory subunit alpha Neighboring gene MPRA-validated peak4643 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:48806609-48807260 Neighboring gene MPRA-validated peak4644 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14340 Neighboring gene PRKAR2A antisense RNA 1 Neighboring gene solute carrier family 25 member 20 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14341 Neighboring gene hESC enhancers GRCh37_chr3:48955152-48955902 and GRCh37_chr3:48955903-48956654 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:48956655-48957405 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:48959089-48959589 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:48961592-48962092 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:48962093-48962593 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19846 Neighboring gene ARIH2 opposite strand lncRNA Neighboring gene ariadne RBR E3 ubiquitin protein ligase 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19847 Neighboring gene MPRA-validated peak4646 silencer Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:49000975-49001622 Neighboring gene uncharacterized LOC124909376 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:49026394-49026957 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:49026958-49027520

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_169732.1 

    Range
    101..150
    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
    48897803..48897852
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    48926808..48926857
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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