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LOC130058749 ATAC-STARR-seq lymphoblastoid silent region 7321 [ Homo sapiens (human) ]

Gene ID: 130058749, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130058749
Gene description
ATAC-STARR-seq lymphoblastoid silent region 7321
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer, transcriptional_cis_regulatory_region
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. An overlapping subregion containing a Neanderthal adaptively introgressed expression-modulating variant (emVar) was additionally validated as an enhancer by MPRAs in K562 erythroleukemia cells, with activity observed for both the introgressed and non-introgressed 16:28986329 or rs117119297 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC130058749 in Genome Data Viewer
Location:
chromosome: 16
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (28974923..28975134)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (29256038..29256249)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (28986244..28986455)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene NFATC2IP antisense RNA 1 Neighboring gene nuclear factor of activated T cells 2 interacting protein Neighboring gene ReSE screen-validated silencer GRCh37_chr16:28973628-28973836 Neighboring gene microRNA 4517 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10653 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10654 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7322 Neighboring gene SPNS lysolipid transporter 1, lysophospholipid Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7323 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7324 Neighboring gene MPRA-validated peak2553 silencer Neighboring gene linker for activation of T cells Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:29036345-29036846 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7325 Neighboring gene nuclear pore complex interacting protein family, member B10, pseudogene

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_43305
  • emVar-containing allelic enhancer experimental_43305

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_193170.2 

    Range
    101..312
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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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    28974923..28975134
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    29256038..29256249
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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