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LOC129995583 ATAC-STARR-seq lymphoblastoid silent region 16814 [ Homo sapiens (human) ]

Gene ID: 129995583, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129995583
Gene description
ATAC-STARR-seq lymphoblastoid silent region 16814
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]
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Genomic context

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See LOC129995583 in Genome Data Viewer
Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (470972..471071)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (329062..329161)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (470972..471071)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes 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 23825 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23826 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23827 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23828 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:324055-324866 Neighboring gene dual specificity phosphatase 22 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23829 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:329543-330742 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 ATAC-STARR-seq lymphoblastoid active region 23839 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:378942-379888 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23841 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16806 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 16809 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16810 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16811 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16812 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16813 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23843 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23842 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 23849 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23850 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23851 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23852 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 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

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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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

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See Variation Viewer (GRCh37.p13)

NCBI Reference Sequences (RefSeq)

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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_175029.1 

    Range
    101..200
    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    470972..471071
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    329062..329161
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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