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LOC130060009 ATAC-STARR-seq lymphoblastoid active region 11529 [ Homo sapiens (human) ]

Gene ID: 130060009, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130060009
Gene description
ATAC-STARR-seq lymphoblastoid active region 11529
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 LOC130060009 in Genome Data Viewer
Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (3967306..3967385)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (3856527..3856606)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (3870600..3870679)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:3807108-3807786 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11522 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11523 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11524 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11525 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11526 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11527 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11528 Neighboring gene purinergic receptor P2X 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:3831158-3832357 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:3833185-3834129 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:3844399-3844898 Neighboring gene ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8025 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:3856267-3857115 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:3860613-3861517 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8026 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8027 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8028 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8029 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:3879079-3879915 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:3879916-3880751 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:3885316-3886231 Neighboring gene long intergenic non-protein coding RNA 1975 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11530 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8030 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8031 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:3910389-3911356 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11531 Neighboring gene zinc finger ZZ-type and EF-hand domain containing 1 Neighboring gene RNA, 5S ribosomal pseudogene 434

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_194430.1 

    Range
    101..180
    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    3967306..3967385
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    3856527..3856606
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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