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LOC129929324 ATAC-STARR-seq lymphoblastoid silent region 217 [ Homo sapiens (human) ]

Gene ID: 129929324, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129929324
Gene description
ATAC-STARR-seq lymphoblastoid silent region 217
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 LOC129929324 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (9292559..9292728)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (8827434..8827603)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (9352618..9352787)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene MIR34A host gene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:9241813-9242673 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 214 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 215 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:9243535-9244395 Neighboring gene long non coding transcriptional activator of miR34a Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9258086-9258606 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9275966-9276493 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 216 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:9300874-9301539 Neighboring gene uncharacterized LOC124903836 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:9308569-9309492 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:9309493-9310416 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9311341-9312263 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:9312526-9313085 Neighboring gene hexose-6-phosphate dehydrogenase/glucose 1-dehydrogenase Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_9566 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 218 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 219 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 220 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9364927-9365774 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:9376867-9377040 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:9377645-9378844 Neighboring gene splA/ryanodine receptor domain and SOCS box containing 1 Neighboring gene Sharpr-MPRA regulatory region 3390 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9410201-9410702 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9410703-9411202 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9412777-9413692 Neighboring gene VISTA enhancer hs1615 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9445249-9445882 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9445883-9446516 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_9573 and experimental_9584 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9459188-9460031 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:9460032-9460874 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:9460875-9461717 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:9472665-9473598 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:9473599-9474530 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9477117-9477617 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 125 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 126 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:9487788-9488422 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 127 Neighboring gene long intergenic non-protein coding RNA 2606

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_162381.1 

    Range
    101..270
    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    9292559..9292728
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    8827434..8827603
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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