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LOC130067832 ATAC-STARR-seq lymphoblastoid silent region 13962 [ Homo sapiens (human) ]

Gene ID: 130067832, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130067832
Gene description
ATAC-STARR-seq lymphoblastoid silent region 13962
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 LOC130067832 in Genome Data Viewer
Location:
chromosome: 22
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (50261652..50261961)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (50768655..50768964)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (50700081..50700390)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50658024-50658666 Neighboring gene tubulin gamma complex component 6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50676935-50677436 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50677437-50677936 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19307 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50682041-50682971 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19309 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13958 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:50685959-50686881 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:50688039-50688885 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13959 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19311 Neighboring gene histone deacetylase 10 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50697131-50697703 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50698428-50698928 Neighboring gene mitogen-activated protein kinase 12 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13960 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13961 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13963 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50700498-50701229 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13964 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13965 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13966 Neighboring gene mitogen-activated protein kinase 11 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:50710106-50710645 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50710646-50711186 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13968 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr22:50720546-50721745 Neighboring gene plexin B2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13969 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19312 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:50738869-50739425 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50739426-50739982 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13970 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr22:50743729-50744928 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:50745236-50745386 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13971 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13972

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_202247.1 

    Range
    101..410
    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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    50261652..50261961
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    50768655..50768964
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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