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LOC129932239 ATAC-STARR-seq lymphoblastoid active region 2328 [ Homo sapiens (human) ]

Gene ID: 129932239, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129932239
Gene description
ATAC-STARR-seq lymphoblastoid active region 2328
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 LOC129932239 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (202159463..202159552)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (201417033..201417122)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (202128591..202128680)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371683 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202099011-202099794 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202099795-202100578 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:202104477-202104684 Neighboring gene G protein-coupled receptor 37 like 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1697 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1698 Neighboring gene ARF like GTPase 8A Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1699 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2327 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2329 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202132551-202133219 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202133799-202134299 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202134943-202135522 Neighboring gene protein tyrosine phosphatase non-receptor type 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202152613-202153112 Neighboring gene protein tyrosine phosphatase receptor type V, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202153807-202154336 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202154337-202154866 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1700 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:202161513-202162316 Neighboring gene small nucleolar RNA U13 Neighboring gene leucine rich repeat containing G protein-coupled receptor 6

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_165275.1 

    Range
    101..190
    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    202159463..202159552
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    201417033..201417122
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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