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LOC132089902 Neanderthal introgressed variant-containing enhancer experimental_19171 [ Homo sapiens (human) ]

Gene ID: 132089902, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132089902
Gene description
Neanderthal introgressed variant-containing enhancer experimental_19171
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 11:117865381 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132089902 in Genome Data Viewer
Location:
chromosome: 11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (117994581..117994750)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (118010960..118011129)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (117865296..117865465)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene FXYD6-FXYD2 readthrough Neighboring gene MED14-independent group 3 enhancer GRCh37_chr11:117712427-117713626 Neighboring gene FXYD6 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:117726457-117726957 Neighboring gene FXYD domain containing ion transport regulator 6 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr11:117738498-117739697 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:117740007-117740526 Neighboring gene Sharpr-MPRA regulatory region 1172 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:117778029-117778529 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:117784655-117785647 Neighboring gene transmembrane serine protease 13 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3939 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5577 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:117802800-117803339 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:117803340-117803878 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_19102 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:117843533-117843947 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_19132 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5579 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3941 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3940 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5580 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:117869597-117870098 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3942 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:117881450-117881950 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5581 Neighboring gene interleukin 10 receptor subunit alpha Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_19207 Neighboring gene small integral membrane protein 35 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5582 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:117935307-117935808 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:117947648-117948243 Neighboring gene RNA, 7SL, cytoplasmic 828, pseudogene Neighboring gene Sharpr-MPRA regulatory region 13014 Neighboring gene uncharacterized LOC105369517 Neighboring gene transmembrane serine protease 4

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_230460.1 

    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    117994581..117994750
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    118010960..118011129
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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