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LOC129935269 ATAC-STARR-seq lymphoblastoid silent region 12187 [ Homo sapiens (human) ]

Gene ID: 129935269, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129935269
Gene description
ATAC-STARR-seq lymphoblastoid silent region 12187
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 LOC129935269 in Genome Data Viewer
Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (190881219..190881278)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (191370323..191370382)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (191745945..191746004)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12183 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12184 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16863 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16864 Neighboring gene NGFI-A binding protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16865 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16866 Neighboring gene uncharacterized LOC124907946 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:191624535-191625734 Neighboring gene CRISPRi-validated cis-regulatory element chr2.5899 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:191655893-191657092 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:191708051-191709250 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12185 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:191734008-191734548 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:191734549-191735087 Neighboring gene uncharacterized LOC124906110 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16867 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12186 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:191746471-191747670 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12189 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12188 Neighboring gene glutaminase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12190 Neighboring gene signal transducer and activator of transcription 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16869 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16870 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16871 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16872 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16873 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12191 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16874 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12192 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16875 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16876 Neighboring gene RAB1A pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16877 Neighboring gene uncharacterized LOC124900514 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:191885525-191886142 Neighboring gene uncharacterized LOC107985785 Neighboring gene STAT4 antisense RNA 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_168284.1 

    Range
    101..160
    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    190881219..190881278
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    191370323..191370382
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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