U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC130058934 ATAC-STARR-seq lymphoblastoid silent region 7442 [ Homo sapiens (human) ]

Gene ID: 130058934, updated on 12-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC130058934
Gene description
ATAC-STARR-seq lymphoblastoid silent region 7442
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 LOC130058934 in Genome Data Viewer
Location:
chromosome: 16
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (46973276..46973355)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (52770095..52770174)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (47007187..47007266)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:46877721-46878246 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:46878247-46878770 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10778 Neighboring gene Sharpr-MPRA regulatory region 14543 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10779 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:46903238-46903844 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:46903845-46904450 Neighboring gene creatine kinase B pseudogene 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:46917671-46918263 Neighboring gene Sharpr-MPRA regulatory region 10353 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:46931211-46931883 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:46933408-46934347 Neighboring gene small nucleolar RNA, C/D box 148 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7437 Neighboring gene glutamic--pyruvic transaminase 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10781 Neighboring gene Sharpr-MPRA regulatory region 12922 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:46963495-46964034 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:46964035-46964572 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:46993862-46994528 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:46999088-46999813 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7439 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7440 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7441 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7443 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10783 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10782 Neighboring gene DnaJ heat shock protein family (Hsp40) member A2 Neighboring gene DNAJA2 divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:47025988-47026488 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7444 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7445 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10784 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10785 Neighboring gene MPRA-validated peak2576 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:47112757-47113521 Neighboring gene neuropilin and tolloid like 2 Neighboring gene small nucleolar RNA U13

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_193355.1 

    Range
    101..180
    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    46973276..46973355
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    52770095..52770174
    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