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LOC132090662 Neanderthal introgressed variant-containing enhancer experimental_7558 [ Homo sapiens (human) ]

Gene ID: 132090662, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132090662
Gene description
Neanderthal introgressed variant-containing enhancer experimental_7558
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 1:37057032 or rs12405687 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132090662 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 (36591346..36591515)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (36454253..36454422)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (37056947..37057116)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:36929292-36930491 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:36931829-36932691 Neighboring gene mitochondrial ribosomal protein S15 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:36946417-36947202 Neighboring gene colony stimulating factor 3 receptor Neighboring gene Sharpr-MPRA regulatory region 4345 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 756 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 757 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:36989208-36989708 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:36989709-36990209 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:36999986-37000486 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:37000487-37000987 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 758 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 759 Neighboring gene Sharpr-MPRA regulatory region 1123 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:37054575-37055075 Neighboring gene ferritin light chain pseudogene 18 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 760 Neighboring gene uncharacterized LOC107984941 Neighboring gene uncharacterized LOC105378648

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_7558

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_231221.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    36591346..36591515
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    36454253..36454422
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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