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LOC132090331 Neanderthal introgressed variant-containing enhancer experimental_40898 [ Homo sapiens (human) ]

Gene ID: 132090331, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132090331
Gene description
Neanderthal introgressed variant-containing enhancer experimental_40898
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 15:74489413 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132090331 in Genome Data Viewer
Location:
chromosome: 15
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (74196987..74197156)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (72062907..72063076)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (74489328..74489497)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903523 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9744 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74464796-74465784 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74465785-74466772 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74466773-74467761 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74468869-74469385 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_40888 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74473477-74474013 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:74476518-74477717 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74485815-74486316 Neighboring gene immunoglobulin superfamily containing leucine rich repeat Neighboring gene signaling receptor and transporter of retinol STRA6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74492227-74492862 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74492863-74493496 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:74495400-74496033 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74497519-74498180 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74498181-74498842 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:74500829-74501490 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:74504651-74505191 Neighboring gene coiled-coil domain containing 33 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:74510918-74511127 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:74515727-74516464 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:74516465-74517202 Neighboring gene uncharacterized LOC105370893 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:74524367-74525566 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74526358-74526954 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74531317-74531912 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74531913-74532508 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74536295-74536796 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74537297-74538296 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74555642-74556474 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74556475-74557305 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74569034-74569758 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74569759-74570483 Neighboring gene VISTA enhancer hs2614 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74593043-74593864 Neighboring gene uncharacterized LOC124903525 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9747 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:74611467-74612377

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_230889.1 

    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    74196987..74197156
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_021160016.1 Reference GRCh38.p14 PATCHES

    Range
    24412..24581
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    72062907..72063076
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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