U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC129937882 ATAC-STARR-seq lymphoblastoid silent region 14877 [ Homo sapiens (human) ]

Gene ID: 129937882, updated on 12-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC129937882
Gene description
ATAC-STARR-seq lymphoblastoid silent region 14877
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]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See LOC129937882 in Genome Data Viewer
Location:
chromosome: 3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (170037970..170038449)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (172822637..172823116)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (169755758..169756237)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20789 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20790 Neighboring gene FHL1 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20791 Neighboring gene NANOG hESC enhancer GRCh37_chr3:169686270-169686802 Neighboring gene SEC62 homolog, preprotein translocation factor Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20792 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14878 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr3:169756663-169757162 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20793 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:169763504-169764004 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20794 Neighboring gene uncharacterized LOC124909455 Neighboring gene G protein-coupled receptor 160 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20795 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20796 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20797 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:169773599-169774098 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20798 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:169779520-169780041 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:169780042-169780562 Neighboring gene RNA, U4 small nuclear 38, pseudogene Neighboring gene KMT5A pseudogene 3

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

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

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See Variation Viewer (GRCh37.p13)

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_170892.1 

    Range
    101..580
    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    170037970..170038449
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    172822637..172823116
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases