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LOC130065663 ATAC-STARR-seq lymphoblastoid silent region 12803 [ Homo sapiens (human) ]

Gene ID: 130065663, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130065663
Gene description
ATAC-STARR-seq lymphoblastoid silent region 12803
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 LOC130065663 in Genome Data Viewer
Location:
chromosome: 20
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (32603261..32603310)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (34328785..34328834)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (31191063..31191112)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene nucleolar protein 4 like Neighboring gene uncharacterized LOC101929698 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:31098781-31099176 Neighboring gene VISTA enhancer hs2225 Neighboring gene Sharpr-MPRA regulatory region 5058 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12791 Neighboring gene uncharacterized LOC105372592 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31124544-31125515 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31126487-31127458 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31128887-31129392 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31129393-31129898 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31149672-31150323 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31151241-31151782 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31158183-31158907 Neighboring gene Sharpr-MPRA regulatory region 4335 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31164325-31165278 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31168247-31168946 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12793 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12794 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12795 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12796 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12797 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12798 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12799 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12800 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12801 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17718 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12802 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31184984-31185484 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31185485-31185985 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31186003-31186504 Neighboring gene NOL4L divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31189553-31190054 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31193059-31193558 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:31193901-31194067 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31198315-31198930 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31198931-31199544 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31206902-31207402 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31211056-31211606 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12804 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:31226322-31226509 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31226763-31227262 Neighboring gene chromosome 20 open reading frame 203 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31235460-31235960 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31235961-31236461 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12805 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17719 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31252264-31252832 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31252833-31253400 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31254622-31255122 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:31259991-31260490 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17721 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31263362-31264064 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31266424-31267023 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31267024-31267622 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31267623-31268222 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr20:31268822-31269421 and GRCh37_chr20:31269422-31270020 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:31271401-31271902 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:31271903-31272402 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31274017-31274656 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31277881-31278443 Neighboring gene BCL2 antagonist/killer 1 pseudogene 1

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_200080.1 

    Range
    101..150
    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    32603261..32603310
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    34328785..34328834
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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