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LOC130067841 ATAC-STARR-seq lymphoblastoid silent region 13971 [ Homo sapiens (human) ]

Gene ID: 130067841, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130067841
Gene description
ATAC-STARR-seq lymphoblastoid silent region 13971
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 LOC130067841 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 (50307478..50307547)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (50815237..50815306)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (50745907..50745976)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50697131-50697703 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50698428-50698928 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 13962 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 mitogen-activated protein kinase 12 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13965 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13966 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 mitogen-activated protein kinase 11 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 13972 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13973 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13974 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19314 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:50753063-50753811 Neighboring gene uncharacterized LOC105373096 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50755814-50756314 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50756315-50756815 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50759389-50759889 Neighboring gene DENN domain containing 6B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13975 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:50770723-50770912 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19316 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19317 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:50780464-50781110 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13976 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13977 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13978 Neighboring gene protein phosphatase 6 regulatory subunit 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19318 Neighboring gene RNA, 7SL, cytoplasmic 500, pseudogene

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_202256.1 

    Range
    101..170
    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
    50307478..50307547
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    50815237..50815306
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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