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LOC132090872 Neanderthal introgressed variant-containing enhancer experimental_36600 [ Homo sapiens (human) ]

Gene ID: 132090872, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132090872
Gene description
Neanderthal introgressed variant-containing enhancer experimental_36600
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). It 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 14:74209097 or rs11624425 variant alleles, and with lower activity for the introgressed rs11624425 'G' variant. CRISPR/Cas9-mediated deletion of a 22 bp subregion centered on rs11624425 indicates that this region positively regulates expression of the MIDEAS (mitotic deacetylase associated SANT domain protein, also known as ELMSAN1) and DNAL1 (dynein axonemal light chain 1) genes. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132090872 in Genome Data Viewer
Location:
chromosome: 14
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (73742309..73742478)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (67949848..67950017)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (74209012..74209181)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene dynein axonemal light chain 1 Neighboring gene Sharpr-MPRA regulatory region 2817 Neighboring gene RNA, U6 small nuclear 240, pseudogene Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_36567 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_36575 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_36590 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8707 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5913 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5914 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8708 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:74185518-74186128 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr14:74190512-74191711 Neighboring gene PNMA family member 1 Neighboring gene mitotic deacetylase associated SANT domain protein Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5915 Neighboring gene uncharacterized LOC124903345 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:74205959-74206474 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:74206989-74207504 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:74207505-74208018 Neighboring gene Sharpr-MPRA regulatory region 4460 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:74213165-74213679 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:74213680-74214193 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8709 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8711 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8710 Neighboring gene Sharpr-MPRA regulatory region 1827 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8713 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5916 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5917 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5918 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8714 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:74228329-74228851 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:74228852-74229373 Neighboring gene microRNA 4505 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8716 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8717 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:74241609-74242167 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5919 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5920 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5921 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8718 Neighboring gene MIDEAS antisense RNA 1 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr14:74262355-74263554 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8719 Neighboring gene small nucleolar RNA U13

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 rs11624425 DNAL1 and MIDEAS cis-regulatory element
  • emVar-containing allelic enhancer experimental_36600

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_231431.1 

    Range
    101..270
    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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    73742309..73742478
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    67949848..67950017
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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