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LOC130002443 ATAC-STARR-seq lymphoblastoid silent region 20210 [ Homo sapiens (human) ]

Gene ID: 130002443, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130002443
Gene description
ATAC-STARR-seq lymphoblastoid silent region 20210
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 LOC130002443 in Genome Data Viewer
Location:
chromosome: 9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (114398039..114398128)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (126590468..126590557)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (117160319..117160408)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:117096322-117096822 Neighboring gene orosomucoid 2 Neighboring gene AT-hook transcription factor Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28855 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28856 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:117129412-117130360 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:117131354-117132058 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_106363 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:117143871-117144852 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:117144987-117145802 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28858 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28859 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28860 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28861 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:117149889-117150624 Neighboring gene uncharacterized LOC124902253 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20211 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:117167737-117168238 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20212 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:117183585-117184085 Neighboring gene whirlin Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:117197109-117197608 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28867 Neighboring gene uncharacterized LOC124902254 Neighboring gene small EDRK-rich factor 2 pseudogene Neighboring gene Sharpr-MPRA regulatory region 12257 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:117266242-117267132 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:117267133-117268023 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:117276161-117276362 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28868 Neighboring gene uncharacterized LOC105376229 Neighboring gene small nucleolar RNA U13

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_181889.1 

    Range
    101..190
    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    114398039..114398128
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    126590468..126590557
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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