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LOC130003992 ATAC-STARR-seq lymphoblastoid silent region 2438 [ Homo sapiens (human) ]

Gene ID: 130003992, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130003992
Gene description
ATAC-STARR-seq lymphoblastoid silent region 2438
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 LOC130003992 in Genome Data Viewer
Location:
chromosome: 10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (69956819..69956888)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (70825321..70825390)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (71716575..71716644)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902444 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr10:71566529-71567728 Neighboring gene uncharacterized LOC105378347 Neighboring gene collagen type XIII alpha 1 chain Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:71602109-71602610 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:71620307-71621012 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:71626613-71627596 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:71627597-71628580 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:71633165-71633944 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:71641515-71642236 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:71662663-71663262 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:71664255-71664755 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2437 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3494 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:71676315-71676994 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:71685663-71686162 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:71706107-71706606 Neighboring gene uncharacterized LOC107984242 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:71721094-71721594 Neighboring gene long intergenic non-protein coding RNA 2636 Neighboring gene macroH2A.2 histone Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:71830815-71831314 Neighboring gene HNF4 motif-containing MPRA enhancer 70 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3495 Neighboring gene AIF family member 2

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_183438.1 

    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    69956819..69956888
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    70825321..70825390
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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