U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC129995564 ATAC-STARR-seq lymphoblastoid silent region 16806 [ Homo sapiens (human) ]

Gene ID: 129995564, updated on 14-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC129995564
Gene description
ATAC-STARR-seq lymphoblastoid silent region 16806
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
Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (391439..391828)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (249823..250212)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374870 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23813 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23814 Neighboring gene MPRA-validated peak5614 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr6:281277-281431 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23815 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23816 Neighboring gene H3K27ac hESC enhancers GRCh37_chr6:291666-292166 and GRCh37_chr6:292167-292667 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23818 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:293614-293770 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23819 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23820 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23821 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23822 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16803 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16804 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:314342-314521 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23823 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23824 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23827 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23826 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23825 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23828 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:324055-324866 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23829 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:329543-330742 Neighboring gene dual specificity phosphatase 22 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23830 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23831 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23832 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16805 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23833 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:342926-343426 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23834 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23835 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:351472-352326 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23836 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23837 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:361141-361640 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23838 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:373619-374192 Neighboring gene MPRA-validated peak5616 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:378942-379888 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23839 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23841 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16807 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16808 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16813 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16812 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16811 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16810 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16809 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23842 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23843 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23844 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23845 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23846 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23847 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23848 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23852 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23851 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23850 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23849 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:434746-434910 Neighboring gene MPRA-validated peak5617 silencer Neighboring gene interferon regulatory factor 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16814 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23854 Neighboring gene MPRA-validated peak5618 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr6:517255-517445 Neighboring gene exocyst complex component 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:551909-552730 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:557275-557462 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:563721-564920 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:582671-583870 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23855 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16815 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23856 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:659114-660062 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:660063-661010 Neighboring gene MARK2 pseudogene 18 Neighboring gene HUS1 checkpoint clamp component B

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 across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. 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

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_175010.1 

    Range
    101..490
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    391439..391828
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    249823..250212
    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