U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC130057352 ATAC-STARR-seq lymphoblastoid silent region 6574 [ Homo sapiens (human) ]

Gene ID: 130057352, updated on 12-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC130057352
Gene description
ATAC-STARR-seq lymphoblastoid silent region 6574
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 LOC130057352 in Genome Data Viewer
Location:
chromosome: 15
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (67066039..67066198)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (64887934..64888093)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (67358377..67358536)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 9309 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:67248284-67249483 Neighboring gene SMAD3 associated long non-coding RNA Neighboring gene ReSE screen-validated silencer GRCh37_chr15:67287649-67287867 Neighboring gene SMAD3 divergent transcript Neighboring gene ReSE screen-validated silencer GRCh37_chr15:67300958-67301136 Neighboring gene high mobility group nucleosomal binding domain 2 pseudogene 47 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_40591 Neighboring gene Sharpr-MPRA regulatory region 4683 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:67322513-67323169 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:67325941-67326548 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:67325333-67325940 Neighboring gene HNF4 motif-containing MPRA enhancer 189 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr15:67356188-67356958 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6573 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:67358498-67359266 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9618 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9619 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9620 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:67381826-67382343 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:67382344-67382860 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9621 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:67386222-67386992 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9622 Neighboring gene SMAD family member 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:67390571-67391072 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9623 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:67398175-67398874 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr15:67399127-67400326 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:67412437-67413294 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9624 Neighboring gene FOXA motif-containing MPRA enhancer 105 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:67438421-67439356 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:67439357-67440291 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:67440670-67441477 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr15:67442285-67443092 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_40599 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_40600 Neighboring gene SMAD3 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:67459191-67459860 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:67459861-67460532 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:67460533-67461202 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9625 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9626 Neighboring gene alpha and gamma adaptin binding protein Neighboring gene ribosomal protein S24 pseudogene 16

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_191773.1 

    Range
    101..260
    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    67066039..67066198
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    64887934..64888093
    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