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LOC130067299 ATAC-STARR-seq lymphoblastoid silent region 13656 [ Homo sapiens (human) ]

Gene ID: 130067299, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130067299
Gene description
ATAC-STARR-seq lymphoblastoid silent region 13656
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 LOC130067299 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 (35381197..35381366)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (35839215..35839384)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (35777190..35777359)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene target of myb1 membrane trafficking protein Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:35732808-35733717 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:35745310-35745842 Neighboring gene microRNA 3909 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:35745843-35746375 Neighboring gene microRNA 6069 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13654 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:35746966-35747474 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:35748292-35749167 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr22:35772530-35773729 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13655 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18904 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18905 Neighboring gene heme oxygenase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18906 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18907 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18908 Neighboring gene minichromosome maintenance complex component 5 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:35821835-35822340 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:35822341-35822848 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:35822849-35823354 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:35831135-35831636 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18909 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:35844065-35845031 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:35845032-35845997 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:35874918-35875095 Neighboring gene tRNA methyltransferase subunit 11-2 pseudogene 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_201714.1 

    Range
    101..270
    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
    35381197..35381366
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    35839215..35839384
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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