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LOC132090748 Neanderthal introgressed variant-containing enhancer experimental_83602 [ Homo sapiens (human) ]

Gene ID: 132090748, updated on 14-Oct-2023

Summary

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Gene symbol
LOC132090748
Gene description
Neanderthal introgressed variant-containing enhancer experimental_83602
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 non-introgressed 5:167881576 or rs954274 variant allele. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132090748 in Genome Data Viewer
Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (168454486..168454655)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (168989267..168989436)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene teneurin transmembrane protein 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23587 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23588 Neighboring gene TENM2 antisense RNA 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16594 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16595 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:167741294-167741817 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23589 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:167754608-167755524 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:167755525-167756441 Neighboring gene uncharacterized LOC124901129 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16597 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:167792124-167792657 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr5:167836336-167837535 Neighboring gene WW and C2 domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23590 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_83610 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_83640 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_83662 Neighboring gene Sharpr-MPRA regulatory region 5384 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:167956617-167957158 Neighboring gene arginyl-tRNA synthetase 1 Neighboring gene fibrillarin like 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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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

General gene information

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Other Names

  • emVar-containing allelic enhancer experimental_83602

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_231307.1 

    Range
    101..270
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    168454486..168454655
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    168989267..168989436
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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