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LOC129995862 ATAC-STARR-seq lymphoblastoid silent region 16949 [ Homo sapiens (human) ]

Gene ID: 129995862, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129995862
Gene description
ATAC-STARR-seq lymphoblastoid silent region 16949
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 LOC129995862 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 (15248442..15248921)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (15121638..15122117)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (15248673..15249152)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374946 Neighboring gene MPRA-validated peak5677 silencer Neighboring gene MPRA-validated peak5678 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:15203770-15204322 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:15207084-15207636 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:15212336-15212500 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:15239058-15239558 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:15239559-15240059 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:15244415-15244928 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16946 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16947 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24064 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24065 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16948 Neighboring gene nonconserved acetylation island sequence 83 enhancer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:15251871-15252646 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24066 Neighboring gene JARID2 antisense RNA 1 Neighboring gene JARID2 divergent transcript Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr6:15264949-15265458 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24067 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:15267598-15268156 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:15268157-15268714 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:15268715-15269273 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:15269274-15269831 Neighboring gene jumonji and AT-rich interaction domain containing 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:15280804-15281784 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24069 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24068 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:15291865-15292366 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24070 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24071 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16950 Neighboring gene Sharpr-MPRA regulatory region 4383 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24072 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24073 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24074 Neighboring gene RNA, U6 small nuclear 522, pseudogene Neighboring gene RNA, U6 small nuclear 645, pseudogene

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_175308.1 

    Range
    101..580
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    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
    15248442..15248921
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    15121638..15122117
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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