U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC129999645 ATAC-STARR-seq lymphoblastoid silent region 18813 [ Homo sapiens (human) ]

Gene ID: 129999645, updated on 12-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC129999645
Gene description
ATAC-STARR-seq lymphoblastoid silent region 18813
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 LOC129999645 in Genome Data Viewer
Location:
chromosome: 7
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (151381367..151381526)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (152554195..152554354)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (151078453..151078612)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:150936637-150937836 Neighboring gene uncharacterized LOC124901779 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150938593-150939094 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150941724-150942298 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150942299-150942872 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150942873-150943447 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150943448-150944021 Neighboring gene Sharpr-MPRA regulatory region 13648 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18809 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150949301-150950210 Neighboring gene SWI/SNF related BAF chromatin remodeling complex subunit D3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150953220-150953720 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150953721-150954221 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150971756-150972555 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150974709-150975418 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:151000420-151001278 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26856 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26858 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26857 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:151038519-151039020 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18812 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26859 Neighboring gene negative regulator of ubiquitin like proteins 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18814 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:151084439-151085101 Neighboring gene WD repeat domain 86 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:151107690-151108322 Neighboring gene WDR86 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:151125597-151126116 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26860 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26861 Neighboring gene uncharacterized LOC124901780 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26862 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26863 Neighboring gene microRNA 3907 Neighboring gene crystallin gamma N

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_179091.1 

    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    151381367..151381526
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    152554195..152554354
    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