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LOC132090458 Neanderthal introgressed variant-containing enhancer experimental_47087 [ Homo sapiens (human) ]

Gene ID: 132090458, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132090458
Gene description
Neanderthal introgressed variant-containing enhancer experimental_47087
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 genetic variant, and was validated as an enhancer by massively parallel reporter assays (MPRAs) in K562 erythroleukemia cells, with activity observed for both the introgressed and non-introgressed 17:16824038 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132090458 in Genome Data Viewer
Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (16920639..16920808)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (16866718..16866887)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (16823953..16824122)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903939 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:16773690-16774683 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:16774796-16775646 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:16775647-16776497 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:16776498-16777348 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:16783154-16783818 Neighboring gene uncharacterized LOC101929105 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:16785977-16786476 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_47083 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:16828359-16829044 Neighboring gene TBC1 domain family member 27, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11772 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11773 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8230 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:16840494-16840994 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:16841792-16842632 Neighboring gene TNF receptor superfamily member 13B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:16846756-16847256 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:16847257-16847757 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:16847819-16848342 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:16848867-16849390 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:16849391-16849914 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11774

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)

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_231016.1 

    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    16920639..16920808
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    16866718..16866887
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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