U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC130062001 ATAC-STARR-seq lymphoblastoid silent region 9190 [ Homo sapiens (human) ]

Gene ID: 130062001, updated on 12-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC130062001
Gene description
ATAC-STARR-seq lymphoblastoid silent region 9190
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 LOC130062001 in Genome Data Viewer
Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (82065816..82065875)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (82932974..82933033)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (80023692..80023751)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:80009332-80010001 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:80022320-80023048 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9188 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9189 Neighboring gene RFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase Neighboring gene G protein pathway suppressor 1 Neighboring gene dihydrouridine synthase 1 like Neighboring gene MPRA-validated peak3028 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:80038893-80039778 Neighboring gene fatty acid synthase Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:80054421-80055336 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9192 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9193 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9194 Neighboring gene small nucleolar RNA, C/D box 134 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:80061739-80062652 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:80062653-80063566 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12986 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12987 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12988 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80065397-80066310 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12989 Neighboring gene coiled-coil domain containing 57 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80074745-80075652 Neighboring gene uncharacterized LOC124904119

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_197083.1 

    Range
    101..160
    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    82065816..82065875
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    82932974..82933033
    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