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LOC132090913 Neanderthal introgressed variant-containing enhancer experimental_61181 [ Homo sapiens (human) ]

Gene ID: 132090913, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132090913
Gene description
Neanderthal introgressed variant-containing enhancer experimental_61181
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 20:62238086 or rs4809313 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132090913 in Genome Data Viewer
Location:
chromosome: 20
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (63606648..63606817)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (65420100..65420269)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (62238001..62238170)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18228 Neighboring gene Sharpr-MPRA regulatory region 13995 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13164 Neighboring gene fibronectin type III domain containing 11 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61120 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18229 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18230 Neighboring gene helicase with zinc finger 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18231 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18232 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18233 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:62202570-62202926 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13165 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62205701-62206428 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:62207026-62207211 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18234 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62213946-62214446 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62214447-62214947 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61137 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61148 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61158 Neighboring gene glucocorticoid modulatory element binding protein 2 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61169 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61184 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61189 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18235 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61197 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62250681-62251180 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61208 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13167 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13168 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61211 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13169 Neighboring gene melanoma highly expressed competing endogenous lncRNA for miR-425 and miR-489 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18236 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62269990-62270750 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13170 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62272271-62273029 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13172 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62273358-62274096 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62275446-62276015 Neighboring gene Sharpr-MPRA regulatory region 12780 Neighboring gene stathmin 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62282910-62283480 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13175 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13176 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62284757-62285436

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_61181

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_231472.1 

    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    63606648..63606817
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    65420100..65420269
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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