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LOC130065818 ATAC-STARR-seq lymphoblastoid silent region 12889 [ Homo sapiens (human) ]

Gene ID: 130065818, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130065818
Gene description
ATAC-STARR-seq lymphoblastoid silent region 12889
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 LOC130065818 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 (37345779..37346078)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (39069854..39070153)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (35974182..35974481)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:35918028-35918932 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17834 Neighboring gene mannosidase beta like Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:35943167-35944074 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:35944075-35944984 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:35947577-35948274 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:35964723-35965222 Neighboring gene uncharacterized LOC105372606 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:35968539-35969071 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17836 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17837 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:35975052-35975552 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17838 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17839 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:35987177-35987747 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17840 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17841 Neighboring gene SRC proto-oncogene, non-receptor tyrosine kinase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17842 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17843 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17844 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12891 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:36019051-36019552 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:36022575-36023431 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:36023432-36024287 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:36024288-36025144 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:36025145-36026001 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:36026002-36026858 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12892 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:36035731-36036650 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:36040408-36040917 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:36040918-36041426 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:36049663-36050276 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:36054060-36054560 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:36054561-36055061 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:36070038-36070538 Neighboring gene ribosomal protein L7a pseudogene 14 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:36114871-36115516 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:36115517-36116161 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17845 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:36146997-36147860 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:36147861-36148724 Neighboring gene BLCAP apoptosis inducing factor Neighboring gene neuronatin

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_200235.1 

    Range
    101..400
    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
    37345779..37346078
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791812.1 Reference GRCh38.p14 PATCHES

    Range
    255281..255580
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    39069854..39070153
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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