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LOC130056738 ATAC-STARR-seq lymphoblastoid silent region 6274 [ Homo sapiens (human) ]

Gene ID: 130056738, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130056738
Gene description
ATAC-STARR-seq lymphoblastoid silent region 6274
Gene type
biological region
Feature type(s)
regulatory: silencer
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 a silencer based on its ability to repress 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 LOC130056738 in Genome Data Viewer
Location:
chromosome: 15
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (34038587..34038646)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (31836774..31836831)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (34330788..34330847)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:33603389-33603900 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:33603901-33604410 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6271 Neighboring gene NANOG hESC enhancer GRCh37_chr15:33620309-33620820 Neighboring gene RYR3 divergent transcript Neighboring gene ryanodine receptor 3 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr15:33837506-33838705 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:33851407-33852197 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr15:33904937-33905438 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:33924098-33924317 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:34012814-34014013 Neighboring gene NANOG hESC enhancer GRCh37_chr15:34030252-34030792 Neighboring gene complement C1q binding protein pseudogene 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:34050593-34051255 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_39317 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:34145183-34146382 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:34150522-34151721 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9171 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9170 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9172 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:34208100-34208650 Neighboring gene apoptosis and caspase activation inhibitor Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6272 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:34277417-34277940 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:34280047-34280546 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:34314668-34315168 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:34315169-34315669 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6273 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6276 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6275 Neighboring gene cholinergic receptor muscarinic 5 Neighboring gene MPRA-validated peak2290 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:34393207-34394064 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9174 Neighboring gene ribosomal protein L32 pseudogene 2 Neighboring gene piggyBac transposable element derived 4 Neighboring gene ER membrane protein complex subunit 7

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_191159.1 

    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    34038587..34038646
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    31836774..31836831
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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