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LOC132089458 Neanderthal introgressed variant-containing enhancer experimental_94418 [ Homo sapiens (human) ]

Gene ID: 132089458, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132089458
Gene description
Neanderthal introgressed variant-containing enhancer experimental_94418
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 6:74354488 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132089458 in Genome Data Viewer
Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (73644680..73644849)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (74822774..74822943)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (74354403..74354572)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17337 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17336 Neighboring gene EEF1A1 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24751 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24752 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:74273247-74273796 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:74275447-74275996 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:74285738-74286453 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:74289636-74290835 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:74291165-74292007 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94401 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94402 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94403 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94405 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:74329139-74329367 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:74333473-74333650 Neighboring gene solute carrier family 17 member 5 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94408 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94411 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94412 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94413 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94414 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94416 Neighboring gene ribosomal protein S27 pseudogene 15 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17338 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24754 Neighboring gene Sharpr-MPRA regulatory region 11313 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24755 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:74405769-74406483 Neighboring gene CD109 antisense RNA 1 Neighboring gene MPRA-validated peak5902 silencer Neighboring gene CD109 molecule Neighboring gene Sharpr-MPRA regulatory region 9272 Neighboring gene MPRA-validated peak5903 silencer Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:74550244-74550817 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:74560911-74561502 Neighboring gene thioredoxin pseudogene 7

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)

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_230017.1 

    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    73644680..73644849
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    74822774..74822943
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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