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LOC130004938 ATAC-STARR-seq lymphoblastoid active region 4192 [ Homo sapiens (human) ]

Gene ID: 130004938, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130004938
Gene description
ATAC-STARR-seq lymphoblastoid active region 4192
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 LOC130004938 in Genome Data Viewer
Location:
chromosome: 10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (125201706..125201825)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (126082727..126082846)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (126890275..126890394)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene C-terminal binding protein 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:126729801-126730300 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:126736559-126737142 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:126740341-126741097 Neighboring gene microRNA 4296 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:126746343-126747091 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:126747092-126747839 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:126750177-126750378 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4191 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:126751552-126752149 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:126767335-126767836 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:126770120-126770948 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:126770949-126771776 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:126773433-126774260 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:126775917-126776743 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:126791223-126792047 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:126795355-126795874 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:126801041-126801540 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:126805494-126806319 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:126824413-126825010 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:126826210-126826808 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:126826809-126827407 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2923 Neighboring gene Sharpr-MPRA regulatory region 360 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:126840048-126841009 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:126849903-126850512 Neighboring gene mitochondrial ribosomal protein S21 pseudogene 6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:126881561-126882062 Neighboring gene VISTA enhancer hs330 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr10:126915977-126917176 Neighboring gene uncharacterized LOC105378541 Neighboring gene NANOG hESC enhancer GRCh37_chr10:126918015-126918529 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr10:126919634-126920833 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr10:126951644-126952843 Neighboring gene uncharacterized LOC105378542 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:126955079-126955580 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:126955581-126956080

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_184383.1 

    Range
    101..220
    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    125201706..125201825
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    126082727..126082846
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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