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LOC132205951 Neanderthal introgressed variant-containing enhancers experimental_7992 and experimental_7995 [ Homo sapiens (human) ]

Gene ID: 132205951, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132205951
Gene description
Neanderthal introgressed variant-containing enhancers experimental_7992 and experimental_7995
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 includes two overlapping subregions containing Neanderthal adaptively introgressed genetic variants, with one having an expression-modulating variant (emVar). Both subregions were validated as enhancers by massively parallel reporter assays (MPRAs) in K562 erythroleukemia cells, with activity observed for both the introgressed and non-introgressed 1:4093449 and 1:4093503 (or rs12041382) variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132205951 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (4033304..4033527)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (3545271..3545494)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (4093364..4093587)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:4015013-4015738 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:4017862-4018398 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:4018399-4018934 Neighboring gene long intergenic non-protein coding RNA 1346 Neighboring gene long intergenic non-protein coding RNA 1345 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:4037314-4037814 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:4037815-4038315 Neighboring gene long intergenic non-protein coding RNA 2780 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:4071131-4071631 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:4086572-4087072 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:4093716-4094491 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:4118474-4118974 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:4118975-4119475 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:4170302-4171501 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:4178536-4179040 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:4179041-4179543 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:4197352-4197952 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:4212141-4212642 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:4212643-4213142 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:4233037-4233538 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:4236159-4236736 Neighboring gene eukaryotic translation elongation factor 1 delta pseudogene 6 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 132 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_8096 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:4388931-4389431 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:4401483-4401984 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:4401985-4402484 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:4440066-4441265 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:4483073-4483573 Neighboring gene long intergenic non-protein coding RNA 1777

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

  • Neanderthal introgressed variant-containing enhancer experimental_7992
  • Neanderthal introgressed variant-containing enhancer experimental_7995
  • emVar-containing allelic enhancer experimental_7995

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_231484.1 

    Range
    101..324
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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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    4033304..4033527
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    3545271..3545494
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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