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LOC129936568 ATAC-STARR-seq lymphoblastoid silent region 14248 [ Homo sapiens (human) ]

Gene ID: 129936568, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129936568
Gene description
ATAC-STARR-seq lymphoblastoid silent region 14248
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 LOC129936568 in Genome Data Viewer
Location:
chromosome: 3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (42654718..42654797)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (42672717..42672796)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (42696210..42696289)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene SEC22 homolog C, vesicle trafficking protein Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:42622926-42623752 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19746 Neighboring gene SS18 like 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14246 Neighboring gene ZBTB47 and NKTR antisense RNA 1 Neighboring gene natural killer cell triggering receptor Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:42672544-42673392 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:42673393-42674241 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19747 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19748 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:42695163-42695804 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14247 Neighboring gene Sharpr-MPRA regulatory region 3469 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:42700825-42701735 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:42701736-42702645 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19749 Neighboring gene zinc finger and BTB domain containing 47 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:42706502-42707002 Neighboring gene uncharacterized LOC124906232 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:42708562-42709098 Neighboring gene RNA, 7SL, cytoplasmic 567, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:42724685-42725186 Neighboring gene Sharpr-MPRA regulatory region 14812 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:42729552-42729776 Neighboring gene kelch like family member 40

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 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_169579.1 

    Range
    101..180
    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    42654718..42654797
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    42672717..42672796
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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