U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC130057553 ATAC-STARR-seq lymphoblastoid silent region 6657 [ Homo sapiens (human) ]

Gene ID: 130057553, updated on 12-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC130057553
Gene description
ATAC-STARR-seq lymphoblastoid silent region 6657
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 LOC130057553 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 (74781960..74782179)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (72651872..72652091)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (75074301..75074520)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene CYP1A1 5' regulatory region Neighboring gene cytochrome P450 family 1 subfamily A member 1 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr15:75021499-75022227 Neighboring gene CYP1A2 5' regulatory region Neighboring gene cytochrome P450 family 1 subfamily A member 2 Neighboring gene dioxin-responsive -38 kb CYP1A2 enhancer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:75059675-75060452 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:75063617-75064332 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:75064333-75065046 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:75066003-75066580 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9790 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9789 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:75070096-75070626 Neighboring gene Sharpr-MPRA regulatory region 4992 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9791 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9792 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6658 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:75075123-75075698 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9794 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9793 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9795 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9796 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:75080141-75080318 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9799 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9800 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9801 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9802 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9803 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9804 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:75084649-75085478 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:75085479-75086307 Neighboring gene C-terminal Src kinase Neighboring gene microRNA 4513 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr15:75090696-75091895 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:75092171-75093022 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:75093023-75093872 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:75112197-75113010 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:75113011-75113824 Neighboring gene lectin, mannose binding 1 like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:75114639-75115451

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_191974.1 

    Range
    101..320
    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
    74781960..74782179
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    72651872..72652091
    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