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LOC130006295 ATAC-STARR-seq lymphoblastoid silent region 3699 [ Homo sapiens (human) ]

Gene ID: 130006295, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130006295
Gene description
ATAC-STARR-seq lymphoblastoid silent region 3699
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 LOC130006295 in Genome Data Viewer
Location:
chromosome: 11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (70203706..70203785)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (70218660..70218739)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (70049812..70049891)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene anoctamin 1 Neighboring gene RNA, U6 small nuclear 1175, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr11:69935765-69935935 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:69938122-69938334 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69939545-69940046 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69940047-69940546 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:69945353-69946112 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:69962362-69962862 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:69962863-69963363 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:69969469-69970107 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:69974897-69975729 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr11:69980445-69981644 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:69986885-69987698 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:69987699-69988510 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70001450-70001950 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70001951-70002451 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:70008633-70008799 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70016639-70017140 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70017141-70017640 Neighboring gene uncharacterized LOC101928473 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:70020559-70021264 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5161 Neighboring gene Sharpr-MPRA regulatory region 13422 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:70042837-70043336 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:70049941-70050132 Neighboring gene uncharacterized LOC124902705 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:70058905-70059714 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:70059715-70060524 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:70060525-70061332 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr11:70065875-70066575 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:70075454-70075954 Neighboring gene Fas associated via death domain Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3700 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3701 Neighboring gene PTPRF interacting protein alpha 1 Neighboring gene H2A.Z histone pseudogene 4

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_185740.1 

    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    70203706..70203785
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    70218660..70218739
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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