U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC130006451 ATAC-STARR-seq lymphoblastoid silent region 3780 [ Homo sapiens (human) ]

Gene ID: 130006451, updated on 12-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC130006451
Gene description
ATAC-STARR-seq lymphoblastoid silent region 3780
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 LOC130006451 in Genome Data Viewer
Location:
chromosome: 11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (76210507..76210676)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (76140223..76140392)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (75921551..75921720)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene UV radiation resistance associated Neighboring gene protein phosphatase 1 regulatory inhibitor subunit 1A pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5282 Neighboring gene RNA, 5S ribosomal pseudogene 344 Neighboring gene MPRA-validated peak1353 silencer Neighboring gene VISTA enhancer hs1435 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:75769360-75769545 Neighboring gene NANOG hESC enhancer GRCh37_chr11:75831587-75832314 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:75863001-75863881 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5284 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:75875819-75876512 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:75886811-75887552 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:75887553-75888295 Neighboring gene Sharpr-MPRA regulatory region 10154 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:75895382-75896163 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:75896164-75896944 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:75897726-75898505 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3778 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:75918003-75918670 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3779 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:75920005-75920671 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:75920672-75921338 Neighboring gene uncharacterized LOC112268079 Neighboring gene CRISPRi-validated cis-regulatory element chr11.4413 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:75946077-75946622 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:75941095-75941596 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:75944436-75944982 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:75945530-75946076 Neighboring gene Wnt family member 11 Neighboring gene long intergenic non-protein coding RNA 2761 Neighboring gene tRNA-Pro (anticodon AGG) 2-4

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_185896.1 

    Range
    101..270
    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    76210507..76210676
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    76140223..76140392
    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