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LOC130056639 ATAC-STARR-seq lymphoblastoid silent region 6202 [ Homo sapiens (human) ]

Gene ID: 130056639, updated on 27-Aug-2024

Summary

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Gene symbol
LOC130056639
Gene description
ATAC-STARR-seq lymphoblastoid silent region 6202
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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Location:
chromosome: 14
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (104800933..104801082)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (99043810..99043959)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107987209 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:105219303-105219804 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:105225732-105226680 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:105226681-105227627 Neighboring gene SIVA1 apoptosis inducing factor Neighboring gene uncharacterized LOC102723342 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:105233884-105234434 Neighboring gene Sharpr-MPRA regulatory region 15301 Neighboring gene AKT serine/threonine kinase 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:105257987-105258628 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:105259269-105259910 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:105259911-105260550 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:105260551-105261192 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6197 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6198 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6199 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:105263234-105264006 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:105264007-105264779 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6200 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6201 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:105270463-105270962 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:105271135-105271884 Neighboring gene zinc finger and BTB domain containing 42 Neighboring gene Sharpr-MPRA regulatory region 3976 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9124 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:105288569-105289200 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6204 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:105293203-105293988 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:105293989-105294774 Neighboring gene VEGFC mRNA stability associated lncRNA Neighboring gene ribosomal protein S26 pseudogene 49

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_191060.1 

    Range
    101..250
    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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    104800933..104801082
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    99043810..99043959
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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