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LOC130066019 ATAC-STARR-seq lymphoblastoid silent region 12980 [ Homo sapiens (human) ]

Gene ID: 130066019, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130066019
Gene description
ATAC-STARR-seq lymphoblastoid silent region 12980
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 LOC130066019 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 (47502127..47502246)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (49240335..49240454)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (46130871..46130990)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17997 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17998 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17999 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12978 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12979 Neighboring gene RNA, U6 small nuclear 497, pseudogene Neighboring gene CRISPRi-validated cis-regulatory element chr20.2047 Neighboring gene RNA, U6 small nuclear 563, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:46152763-46153530 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:46158187-46158687 Neighboring gene nuclear receptor coactivator 3 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:46190110-46190292 Neighboring gene MPRA-validated peak4234 silencer Neighboring gene ribosomal protein S3A pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:46276897-46277614 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr20:46277615-46278332 Neighboring gene nuclear receptor coactivator 3 repeat instability region Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18000 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18001 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:46293563-46294548 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18002 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:46294549-46295532 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18003 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18004 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:46303203-46304168 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:46307531-46308031 Neighboring gene sulfatase 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:46316712-46317262 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:46317263-46317814 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:46326206-46326710 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18005 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:46339340-46339840 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:46339841-46340341 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18006 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:46381087-46381588 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:46381589-46382088 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:46386138-46386895 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:46386896-46387654 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:46387655-46388411 Neighboring gene NANOG hESC enhancer GRCh37_chr20:46390145-46390683 Neighboring gene Sharpr-MPRA regulatory region 8498 Neighboring gene uncharacterized LOC124904922

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_200436.1 

    Range
    101..220
    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
    47502127..47502246
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    49240335..49240454
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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