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LOC132089400 Neanderthal introgressed variant-containing enhancer experimental_92132 [ Homo sapiens (human) ]

Gene ID: 132089400, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132089400
Gene description
Neanderthal introgressed variant-containing enhancer experimental_92132
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 the non-introgressed 6:52417100 variant allele. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132089400 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 (52552217..52552386)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (52390996..52391165)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (52417015..52417184)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17283 Neighboring gene progestin and adipoQ receptor family member 8 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24676 Neighboring gene VISTA enhancer hs2064 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24678 Neighboring gene Sharpr-MPRA regulatory region 10279 Neighboring gene uncharacterized LOC124901331 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:52285109-52285700 Neighboring gene EF-hand domain containing 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:52362612-52362813 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24679 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:52368564-52369763 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24680 Neighboring gene translocation associated membrane protein 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:52389524-52390029 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:52390030-52390534 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24681 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24682 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24683 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24684 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24685 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:52438134-52438662 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24686 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17284 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17285 Neighboring gene TRAM2 antisense RNA 1 (head to head) Neighboring gene FOXA motif-containing MPRA enhancer 62 Neighboring gene uncharacterized LOC124901330

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_229959.1 

    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
    52552217..52552386
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    52390996..52391165
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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