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LOC130007930 ATAC-STARR-seq lymphoblastoid silent region 4473 [ Homo sapiens (human) ]

Gene ID: 130007930, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130007930
Gene description
ATAC-STARR-seq lymphoblastoid silent region 4473
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 LOC130007930 in Genome Data Viewer
Location:
chromosome: 12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (51814437..51814516)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (51777963..51778042)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (52208221..52208300)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4468 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4469 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6382 Neighboring gene solute carrier family 4 member 8 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:51826488-51826988 Neighboring gene SLC4A8 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4470 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:51895635-51896136 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:51896137-51896636 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6383 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6384 Neighboring gene NANOG hESC enhancer GRCh37_chr12:51938922-51939423 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4471 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4472 Neighboring gene sodium voltage-gated channel alpha subunit 8 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:52039206-52040092 Neighboring gene SCN8A eExon liver enhancer Neighboring gene heterogeneous nuclear ribonucleoprotein A3 pseudogene 10 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:52208409-52208908 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4474 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:52220360-52220860 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:52221534-52222085 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:52223188-52223737 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:52229864-52230815 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:52238698-52239408 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:52239409-52240117 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:52240828-52241536 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:52241735-52242726 Neighboring gene fidgetin like 2 Neighboring gene transmembrane and death domain 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:52256788-52257308 Neighboring gene FIGNL2 divergent transcript Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:52262827-52263460 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:52263461-52264092 Neighboring gene ankyrin repeat domain 33

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_188501.1 

    Range
    101..180
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    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    51814437..51814516
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    51777963..51778042
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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