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LOC129998568 ATAC-STARR-seq lymphoblastoid silent region 18232 [ Homo sapiens (human) ]

Gene ID: 129998568, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129998568
Gene description
ATAC-STARR-seq lymphoblastoid silent region 18232
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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Location:
chromosome: 7
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (70726928..70726977)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (71950578..71950627)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (70191914..70191963)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene activator of transcription and developmental regulator AUTS2 Neighboring gene uncharacterized LOC124901668 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:70061071-70061572 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr7:70079304-70079836 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:70095779-70096557 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:70096558-70097335 Neighboring gene VISTA enhancer hs925 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26110 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:70111719-70112218 Neighboring gene MPRA-validated peak6564 silencer Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:70145703-70146628 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:70146629-70147554 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18226 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18227 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18228 Neighboring gene uncharacterized LOC107986709 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18231 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18229 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18230 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr7:70164947-70165914 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:70168599-70169443 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:70176010-70176532 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26111 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr7:70189901-70190592 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:70193883-70194402 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:70193362-70193882 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18233 Neighboring gene uncharacterized LOC105375347 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:70227272-70227983 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26112 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18234 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18235 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:70300982-70302181 Neighboring gene neuroepithelial cell transforming 1 pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:70303269-70304021

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_178014.1 

    Range
    101..150
    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    70726928..70726977
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    71950578..71950627
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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