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LOC129930119 ATAC-STARR-seq lymphoblastoid silent region 648 [ Homo sapiens (human) ]

Gene ID: 129930119, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129930119
Gene description
ATAC-STARR-seq lymphoblastoid silent region 648
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 LOC129930119 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 (35808389..35808638)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (35671278..35671527)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (36273990..36274239)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 7840 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 645 Neighboring gene Sharpr-MPRA regulatory region 10959 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:36191359-36191542 Neighboring gene chromosome 1 open reading frame 216 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:36204140-36205339 Neighboring gene claspin Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 646 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 737 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:36272791-36273290 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 647 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 738 Neighboring gene argonaute RISC component 4 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:36315018-36315170 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 649 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr1:36351383-36352022 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 739 Neighboring gene CFAP97 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 740 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:36359789-36360988 Neighboring gene argonaute RISC component 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:36396322-36396845 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:36396846-36397370 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:36397371-36397893 Neighboring gene argonaute RISC catalytic component 3 Neighboring gene NANOG hESC enhancer GRCh37_chr1:36474078-36474579 Neighboring gene uncharacterized LOC105378647

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_163172.1 

    Range
    101..350
    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
    35808389..35808638
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    35671278..35671527
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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