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LOC130066646 ATAC-STARR-seq lymphoblastoid active region 18444 [ Homo sapiens (human) ]

Gene ID: 130066646, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130066646
Gene description
ATAC-STARR-seq lymphoblastoid active region 18444
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 LOC130066646 in Genome Data Viewer
Location:
chromosome: 21
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (37208302..37208491)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (35590523..35590712)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (38580603..38580792)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13296 Neighboring gene Sharpr-MPRA regulatory region 5899 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13298 Neighboring gene phosphatidylinositol glycan anchor biosynthesis class P Neighboring gene tetratricopeptide repeat domain 3 Neighboring gene GFI1 motif-containing MPRA enhancer 103 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:38519638-38520138 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18443 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr21:38567734-38568933 Neighboring gene TTC3 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:38579468-38580304 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18445 Neighboring gene RNA, 7SL, cytoplasmic 678, pseudogene Neighboring gene Down syndrome critical region 9 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18446 Neighboring gene VPS26 endosomal protein sorting factor C Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18447 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:38629775-38630367 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:38630368-38630960 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13299 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18449 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13300

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_201062.1 

    Range
    101..290
    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_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    37208302..37208491
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    35590523..35590712
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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