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LOC130063167 ATAC-STARR-seq lymphoblastoid active region 13745 [ Homo sapiens (human) ]

Gene ID: 130063167, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130063167
Gene description
ATAC-STARR-seq lymphoblastoid active region 13745
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 LOC130063167 in Genome Data Viewer
Location:
chromosome: 19
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (3821800..3821959)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (3801072..3801231)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (3821798..3821957)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3770519-3771018 Neighboring gene MPRA-validated peak3254 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3784812-3785807 Neighboring gene retina and anterior neural fold homeobox 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:3787338-3787536 Neighboring gene MPRA-validated peak3255 silencer Neighboring gene megakaryocyte-associated tyrosine kinase Neighboring gene ReSE screen-validated silencer GRCh37_chr19:3809153-3809388 Neighboring gene Sharpr-MPRA regulatory region 15218 Neighboring gene MPRA-validated peak3257 silencer Neighboring gene zinc finger RNA binding protein 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3831251-3831840 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3843229-3843728 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3849523-3850024 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3871123-3871622 Neighboring gene Sharpr-MPRA regulatory region 13254 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3880358-3880888 Neighboring gene ferritin light chain pseudogene 5 Neighboring gene ATCAY kinesin light chain interacting caytaxin Neighboring gene ReSE screen-validated silencer GRCh37_chr19:3912272-3912471 Neighboring gene RNA, 7SL, cytoplasmic 202, pseudogene

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 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_197584.1 

    Range
    101..260
    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    3821800..3821959
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    3801072..3801231
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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