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LOC132090856 Neanderthal introgressed variant-containing enhancer experimental_23722 [ Homo sapiens (human) ]

Gene ID: 132090856, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132090856
Gene description
Neanderthal introgressed variant-containing enhancer experimental_23722
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 the introgressed 12:104472365 or rs17192854 variant allele. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132090856 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 (104078502..104078671)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (104040194..104040363)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (104472280..104472449)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6904 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6905 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23620 Neighboring gene thymine DNA glycosylase Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23681 Neighboring gene glycosyltransferase 8 domain containing 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:104408145-104408367 Neighboring gene phosphoglycerate mutase 1 (brain) pseudogene Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23711 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23714 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4784 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:104458005-104458174 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4785 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4786 Neighboring gene host cell factor C2 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23731 Neighboring gene RNA, 5S ribosomal pseudogene 370 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:104530547-104531140 Neighboring gene nuclear transcription factor Y subunit beta Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:104531141-104531732 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4789 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4790 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23735 Neighboring gene uncharacterized LOC105369947

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_23722

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_231415.1 

    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    104078502..104078671
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    104040194..104040363
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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