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LOC129929850 ATAC-STARR-seq lymphoblastoid active region 529 [ Homo sapiens (human) ]

Gene ID: 129929850, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129929850
Gene description
ATAC-STARR-seq lymphoblastoid active region 529
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 LOC129929850 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 (26890357..26890626)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (26728420..26728689)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (27216848..27217117)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:27189325-27190204 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 526 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 527 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:27195686-27195844 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:27198339-27199538 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:27201365-27201864 Neighboring gene stratifin Neighboring gene GPN-loop GTPase 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27215935-27216812 Neighboring gene G-patch domain containing 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 530 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:27232113-27232613 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:27232651-27233152 Neighboring gene nuclear distribution C, dynein complex regulator Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:27241933-27242433 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:27245085-27245285 Neighboring gene nuclear receptor subfamily 0 group B member 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 496 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 531 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:27248501-27249042 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 497 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 498 Neighboring gene Sharpr-MPRA regulatory region 10310 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27286397-27287079 Neighboring gene keratinocyte differentiation factor 1

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_162903.1 

    Range
    101..370
    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
    26890357..26890626
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    26728420..26728689
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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