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LOC132090540 Neanderthal introgressed variant-containing enhancer experimental_51043 [ Homo sapiens (human) ]

Gene ID: 132090540, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132090540
Gene description
Neanderthal introgressed variant-containing enhancer experimental_51043
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 19:33596749 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132090540 in Genome Data Viewer
Location:
chromosome: 19
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (33105758..33105927)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (35624444..35624613)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (33596664..33596833)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14436 Neighboring gene FA core complex associated protein 24 Neighboring gene rhophilin Rho GTPase binding protein 2 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:33522974-33523845 Neighboring gene HNF1 motif-containing MPRA enhancer 165 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:33532539-33533040 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:33534226-33534776 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:33539186-33539904 Neighboring gene uncharacterized LOC124904805 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:33545753-33546253 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:33547387-33547910 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:33547911-33548434 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:33554488-33555116 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10488 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10489 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:33556329-33556828 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_51002 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_51016 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14437 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:33573947-33574447 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_51021 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_51032 Neighboring gene G-patch domain containing 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_51054 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_51091 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:33619955-33620099 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_51096 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10490 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14438 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14439 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_51125 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_51126 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_51137 Neighboring gene WD repeat domain 88 Neighboring gene uncharacterized LOC124904691 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14440 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_51151 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:33666856-33667620 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10491 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10492 Neighboring gene tRNA-Thr (anticodon AGT) 1-3

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_231098.1 

    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    33105758..33105927
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    35624444..35624613
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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