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LOC132090454 Neanderthal introgressed variant-containing enhancer experimental_46971 [ Homo sapiens (human) ]

Gene ID: 132090454, updated on 14-Oct-2023

Summary

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Gene symbol
LOC132090454
Gene description
Neanderthal introgressed variant-containing enhancer experimental_46971
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 17:12594859 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132090454 in Genome Data Viewer
Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (12691457..12691626)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (12598928..12599097)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene mitogen-activated protein kinase kinase 4 Neighboring gene dynein light chain Tctex-type 1 pseudogene Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr17:12125284-12125872 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:12287658-12287861 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11736 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:12358360-12358972 Neighboring gene Sharpr-MPRA regulatory region 9419 Neighboring gene uncharacterized LOC105371540 Neighboring gene long intergenic non-protein coding RNA 670 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:12533784-12534983 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:12540895-12541394 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:12591458-12591958 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:12591959-12592459 Neighboring gene MYOCD antisense RNA 1 Neighboring gene ARHGAP44 and MYOCD antisense RNA 1 Neighboring gene myocardin Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8206 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11737 Neighboring gene Rho GTPase activating protein 44 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11738 Neighboring gene microRNA 1269b

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

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_231012.1 

    Range
    101..270
    Download
    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    12691457..12691626
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    12598928..12599097
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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