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LOC130006248 ATAC-STARR-seq lymphoblastoid silent region 3667 [ Homo sapiens (human) ]

Gene ID: 130006248, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130006248
Gene description
ATAC-STARR-seq lymphoblastoid silent region 3667
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 LOC130006248 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 (68312216..68312505)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (68316649..68316938)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (68079684..68079973)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene MPRA-validated peak1319 silencer Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr11:68034746-68035945 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:68039550-68040404 Neighboring gene chromosome 11 open reading frame 24 Neighboring gene uncharacterized LOC105369363 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3666 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5133 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5134 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:68066209-68066956 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:68067706-68068453 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:68080045-68080920 Neighboring gene uncharacterized LOC124900302 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:68080921-68081795 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:68082507-68083006 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:68084075-68084742 Neighboring gene LDL receptor related protein 5 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:68095823-68096400 Neighboring gene uncharacterized LOC124902698 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:68099859-68100434

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 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_185693.1 

    Range
    101..390
    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
    68312216..68312505
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    68316649..68316938
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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