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LOC129929187 ATAC-STARR-seq lymphoblastoid silent region 112 [ Homo sapiens (human) ]

Gene ID: 129929187, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129929187
Gene description
ATAC-STARR-seq lymphoblastoid silent region 112
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 LOC129929187 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 (2388631..2388800)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (1827900..1828069)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (2320070..2320239)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903824 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 110 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:2246747-2247500 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:2253541-2254148 Neighboring gene MORN repeat containing 1 Neighboring gene small nuclear ribonucleoprotein polypeptide N pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr1:2306674-2306868 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 54 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 55 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 56 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 113 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 114 Neighboring gene Sharpr-MPRA regulatory region 13804 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:2340121-2340621 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:2342650-2343230 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr1:2343231-2343811 to GRCh37_chr1:2344393-2344972 Neighboring gene retention in endoplasmic reticulum sorting receptor 1 Neighboring gene peroxisomal biogenesis factor 10 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:2361610-2361787 Neighboring gene phospholipase C eta 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:2377030-2377864 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:2378700-2379534 Neighboring gene Sharpr-MPRA regulatory region 13638 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:2383066-2383714 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:2383715-2384362 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:2423421-2423982 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:2430511-2431710

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_162244.1 

    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
    2388631..2388800
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    1827900..1828069
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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