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LOC130007338 ATAC-STARR-seq lymphoblastoid silent region 4219 [ Homo sapiens (human) ]

Gene ID: 130007338, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130007338
Gene description
ATAC-STARR-seq lymphoblastoid silent region 4219
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 LOC130007338 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 (8914551..8914600)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (8896796..8896845)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (9067147..9067196)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:8940741-8941280 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:8941281-8941820 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr12:8941899-8942576 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr12:8942577-8943254 Neighboring gene A2ML1 antisense RNA 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:8947958-8948568 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:8957581-8958288 Neighboring gene long intergenic non-protein coding RNA 2972 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:8958995-8959702 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:8962654-8963394 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:8963395-8964136 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:8967023-8967549 Neighboring gene Sharpr-MPRA regulatory region 8322 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:8980966-8981708 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:8984681-8985424 Neighboring gene alpha-2-macroglobulin like 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:9057572-9058228 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:9060851-9061506 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:9064238-9064790 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4218 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4220 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:9101505-9102410 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:9102411-9103315 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:9108425-9109624 Neighboring gene polyhomeotic homolog 1 Neighboring gene mannose-6-phosphate receptor, cation dependent Neighboring gene killer cell lectin like receptor G1 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 34

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_187989.1 

    Range
    101..150
    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    8914551..8914600
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    8896796..8896845
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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