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LOC130008485 ATAC-STARR-seq lymphoblastoid active region 6815 [ Homo sapiens (human) ]

Gene ID: 130008485, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130008485
Gene description
ATAC-STARR-seq lymphoblastoid active region 6815
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 LOC130008485 in Genome Data Viewer
Location:
chromosome: 12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (95731819..95731878)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (95710973..95711032)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (96125597..96125656)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene MPRA-validated peak1899 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:95916458-95916958 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:95936387-95936886 Neighboring gene ubiquitin specific peptidase 44 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6811 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:96004940-96005508 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr12:96005509-96006077 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:96008766-96009393 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:96016523-96017477 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4739 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:96026735-96027934 Neighboring gene Sharpr-MPRA regulatory region 15569 Neighboring gene phosphoglycerate mutase 1 pseudogene 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:96087614-96088118 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:96088119-96088623 Neighboring gene netrin 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6812 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6813 Neighboring gene uncharacterized LOC105369919 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:96125327-96125544 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 12:96134654 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 12:96141252 Neighboring gene RNA, U6 small nuclear 247, pseudogene Neighboring gene SNRPF divergent transcript Neighboring gene long intergenic non-protein coding RNA 2410

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_187054.1 

    Range
    101..160
    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    95731819..95731878
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    95710973..95711032
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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