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LOC130007625 ATAC-STARR-seq lymphoblastoid silent region 4322 [ Homo sapiens (human) ]

Gene ID: 130007625, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130007625
Gene description
ATAC-STARR-seq lymphoblastoid silent region 4322
Gene type
biological region
Feature type(s)
regulatory: enhancer, 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 includes an accessible chromatin subregion 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. This locus also includes a subregion containing a Neanderthal adaptively introgressed genetic variant. That subregion was validated as an enhancer by MPRAs in K562 erythroleukemia cells, with activity observed for both the introgressed and non-introgressed 12:30907427 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC130007625 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 (30754408..30755184)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (30629045..30629821)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (30907342..30908118)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105369719 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_28131 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:30756793-30757482 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:30757483-30758172 Neighboring gene importin 8 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4321 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6158 Neighboring gene caprin family member 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6159 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:30909210-30909413 Neighboring gene uncharacterized LOC645485 Neighboring gene NANOG hESC enhancer GRCh37_chr12:30938423-30938924 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:30945898-30946399 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:30946901-30947402 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:30947403-30947902 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:30948405-30948904 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:30948905-30949406 Neighboring gene long intergenic non-protein coding RNA 941 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:30989687-30990886 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:31001273-31001817 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6160 Neighboring gene peptidylprolyl isomerase A pseudogene 44

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. Detection of Neanderthal Adaptively Introgressed Genetic Variants That Modulate Reporter Gene Expression in Human Immune Cells. Jagoda E, et al. Mol Biol Evol, 2022 Jan 7. PMID 34662402, Free PMC Article
  2. 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)

General gene information

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Other Names

  • Neanderthal introgressed variant-containing enhancer experimental_28171

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_188247.2 

    Range
    101..877
    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
    30754408..30755184
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    30629045..30629821
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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