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LOC130060837 ATAC-STARR-seq lymphoblastoid active region 12158 [ Homo sapiens (human) ]

Gene ID: 130060837, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130060837
Gene description
ATAC-STARR-seq lymphoblastoid active region 12158
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 LOC130060837 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 (40599099..40599398)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (41463477..41463776)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (38755351..38755650)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985090 Neighboring gene CRISPRi-validated cis-regulatory element chr17.2443 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12147 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12148 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8494 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12149 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12150 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12151 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:38716282-38716799 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12152 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12153 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12154 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:38720363-38721279 Neighboring gene C-C motif chemokine receptor 7 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12155 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:38738644-38738789 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr17:38744874-38746073 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12157 Neighboring gene Sharpr-MPRA regulatory region 2180 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12159 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12160 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12161 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12162 Neighboring gene SWI/SNF related BAF chromatin remodeling complex subunit E1 Neighboring gene Sharpr-MPRA regulatory region 7873 Neighboring gene keratin 222

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_196093.1 

    Range
    101..400
    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
    40599099..40599398
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    41463477..41463776
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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