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LOC132090866 Neanderthal introgressed variant-containing enhancer experimental_33558 [ Homo sapiens (human) ]

Gene ID: 132090866, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132090866
Gene description
Neanderthal introgressed variant-containing enhancer experimental_33558
Gene type
biological region
Feature type(s)
regulatory: enhancer, 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 region contains a Neanderthal adaptively introgressed expression-modulating variant (emVar), and was validated as a functional enhancer by massively parallel reporter assays (MPRAs) in K562 erythroleukemia cells, with activity observed for both the introgressed and non-introgressed 13:99804376 or rs61968301 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132090866 in Genome Data Viewer
Location:
chromosome: 13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (99152037..99152206)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (98362186..98362355)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (99804291..99804460)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene dedicator of cytokinesis 9 Neighboring gene RNA, U6 small nuclear 83, pseudogene Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr13:99719017-99720216 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7924 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7925 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5462 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:99738979-99739540 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5465 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:99740103-99740662 Neighboring gene ReSE screen-validated silencer GRCh37_chr13:99752082-99752247 Neighboring gene DOCK9 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7926 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7927 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5466 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5467 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr13:99811198-99812397 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:99824919-99825420 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7928 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:99833707-99834219 Neighboring gene ribosomal protein S6 pseudogene 23 Neighboring gene glyceraldehyde 3 phosphate dehydrogenase pseudogene 22

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

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

  • emVar-containing allelic enhancer experimental_33558

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_231425.1 

    Range
    101..270
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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_000013.11 Reference GRCh38.p14 Primary Assembly

    Range
    99152037..99152206
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    98362186..98362355
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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