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LOC129932160 ATAC-STARR-seq lymphoblastoid silent region 1664 [ Homo sapiens (human) ]

Gene ID: 129932160, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129932160
Gene description
ATAC-STARR-seq lymphoblastoid silent region 1664
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 LOC129932160 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 (197902835..197903084)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (197162231..197162480)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (197871965..197872214)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene DENN domain containing 1B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1661 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1662 Neighboring gene Sharpr-MPRA regulatory region 12429 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2276 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:197757007-197757507 Neighboring gene RPL24 pseudogene 5 Neighboring gene family with sequence similarity 204 member B, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:197769368-197770108 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:197771590-197772329 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:197779872-197780608 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:197782608-197783566 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:197783567-197784524 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:197859970-197860527 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1663 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:197887073-197887799 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:197890605-197891127 Neighboring gene chromosome 1 open reading frame 53 Neighboring gene LIM homeobox 9 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:198001212-198001386 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:198025825-198026449 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2278 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2277 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2279 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1665 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2280 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2281 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2282 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1666 Neighboring gene NIMA related kinase 7 Neighboring gene proline rich 13 pseudogene 1

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_165199.1 

    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
    197902835..197903084
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    197162231..197162480
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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