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LOC132088604 Neanderthal introgressed variant-containing enhancer experimental_1534 [ Homo sapiens (human) ]

Gene ID: 132088604, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132088604
Gene description
Neanderthal introgressed variant-containing enhancer experimental_1534
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 1:19698218 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132088604 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 (19371639..19371808)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (19195176..19195345)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (19698133..19698302)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903867 Neighboring gene RNA, U6 small nuclear 1099, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:19638229-19638728 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 353 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19641943-19642442 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:19644916-19645106 Neighboring gene aldo-keto reductase family 7 member A2 Neighboring gene solute carrier family 66 member 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19661163-19661664 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19661665-19662164 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:19663848-19664812 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19665979-19666480 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19667246-19668220 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 299 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:19679737-19680421 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19682496-19682996 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19682997-19683497 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_1531 Neighboring gene capping actin protein of muscle Z-line subunit beta Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19685462-19685962 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:19696541-19697233 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 300 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 301 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:19727675-19728354 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:19729033-19729710 Neighboring gene uncharacterized LOC124903868 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19745938-19746438 Neighboring gene RNA, 7SL, cytoplasmic 277, pseudogene

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_229163.1 

    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
    19371639..19371808
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    19195176..19195345
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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