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LOC130067562 ATAC-STARR-seq lymphoblastoid silent region 13801 [ Homo sapiens (human) ]

Gene ID: 130067562, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130067562
Gene description
ATAC-STARR-seq lymphoblastoid silent region 13801
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 LOC130067562 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 (41871964..41872043)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (42350742..42350821)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (42267968..42268047)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene meiotic double-stranded break formation protein 1 Neighboring gene RNA, U6atac small nuclear 22, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19129 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19130 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19131 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19132 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19133 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:42195504-42196490 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13798 Neighboring gene coiled-coil domain containing 134 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19136 Neighboring gene NANOG hESC enhancer GRCh37_chr22:42219786-42220287 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:42222133-42222639 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:42226556-42227096 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:42227097-42227636 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:42228578-42229234 Neighboring gene SREBF2 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13800 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:42231025-42231526 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:42231527-42232026 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:42242468-42243268 Neighboring gene sterol regulatory element binding transcription factor 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:42258655-42259155 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:42303627-42304294 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13802 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13803 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13804 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:42310379-42311304 Neighboring gene microRNA 33a Neighboring gene shisa family member 8

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_201977.1 

    Range
    101..180
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    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
    41871964..41872043
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    42350742..42350821
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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