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LOC129938231 ATAC-STARR-seq lymphoblastoid active region 21050 [ Homo sapiens (human) ]

Gene ID: 129938231, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129938231
Gene description
ATAC-STARR-seq lymphoblastoid active region 21050
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 LOC129938231 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 (195155282..195155421)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (197853162..197853301)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (194876011..194876150)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene xyloside xylosyltransferase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21047 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21048 Neighboring gene uncharacterized LOC105374296 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21049 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:194873291-194873932 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:194873933-194874573 Neighboring gene XXYLT1 antisense RNA 2 Neighboring gene RNA, 7SL, cytoplasmic 36, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:194880491-194880991 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:194881004-194881518 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21051 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21052 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:194884078-194884245 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:194900787-194901364 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:194901365-194901942 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:194904967-194906166 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:194908389-194908904 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:194927427-194927954 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:194927955-194928480 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:194932550-194933131 Neighboring gene RNA, U6 small nuclear 25, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:194947105-194947699 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:194960771-194961333 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15031 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21053 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:194974283-194975070 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:194976828-194977002 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15032 Neighboring gene uncharacterized LOC124909475

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_171241.1 

    Range
    101..240
    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
    195155282..195155421
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    197853162..197853301
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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