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LOC129930495 ATAC-STARR-seq lymphoblastoid silent region 856 [ Homo sapiens (human) ]

Gene ID: 129930495, updated on 14-Oct-2023

Summary

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Gene symbol
LOC129930495
Gene description
ATAC-STARR-seq lymphoblastoid silent region 856
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 LOC129930495 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (47436524..47436683)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (47314991..47315150)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1389 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_8190 Neighboring gene forkhead box E3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 855 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:47899798-47900313 Neighboring gene FOXD2 adjacent opposite strand RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 857 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 858 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:47905134-47905903 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:47911867-47912367 Neighboring gene forkhead box D2 Neighboring gene ribosomal protein L21 pseudogene 24

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

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_163546.1 

    Range
    101..260
    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    47436524..47436683
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    47314991..47315150
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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