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LOC132089546 Neanderthal introgressed variant-containing enhancer experimental_99443 [ Homo sapiens (human) ]

Gene ID: 132089546, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132089546
Gene description
Neanderthal introgressed variant-containing enhancer experimental_99443
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 7:50669123 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132089546 in Genome Data Viewer
Location:
chromosome: 7
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (50601341..50601510)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (50762486..50762655)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (50669038..50669207)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:50514049-50515248 Neighboring gene Sharpr-MPRA regulatory region 9826 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18183 Neighboring gene fidgetin like 1 Neighboring gene VISTA enhancer hs2059 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr7:50569579-50570080 and GRCh37_chr7:50570081-50570580 Neighboring gene dopa decarboxylase Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:50581285-50581919 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_99424 and experimental_99425 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr7:50598907-50600106 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:50602470-50603669 Neighboring gene DDC antisense RNA 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:50637965-50638490 Neighboring gene growth factor receptor bound protein 10 Neighboring gene uncharacterized LOC124901632 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:50720584-50721214 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_99457 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_99465 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:50736937-50737438 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:50737439-50737938 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:50782907-50783422 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_99483 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:50836560-50837139 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:50837140-50837720 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:50875755-50876262 Neighboring gene Sharpr-MPRA regulatory region 14531 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:50894096-50895295 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:50905976-50907175 Neighboring gene ribosomal protein L39 pseudogene 23

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_230105.1 

    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    50601341..50601510
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    50762486..50762655
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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