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LOC132088805 Neanderthal introgressed variant-containing enhancer experimental_56698 [ Homo sapiens (human) ]

Gene ID: 132088805, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132088805
Gene description
Neanderthal introgressed variant-containing enhancer experimental_56698
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 2:179947564 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132088805 in Genome Data Viewer
Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (179082752..179082921)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (179565954..179566123)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (179947479..179947648)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene coiled-coil domain containing 141 Neighboring gene uncharacterized LOC105373766 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16812 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16813 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16814 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16815 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16816 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16817 Neighboring gene ribosomal protein S6 pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16818 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:179922464-179923068 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:179931204-179931704 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_56700 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_56701 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12152 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16819 Neighboring gene MPRA-validated peak3949 silencer Neighboring gene MPRA-validated peak3950 silencer Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_56707 Neighboring gene small nucleolar RNA U13 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_56714 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_56716 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_56717 Neighboring gene SEC14 and spectrin domain containing 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_56718 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_56719 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_56720 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_56724 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:180060941-180061440 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16820 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12154 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12153 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:180128689-180128852 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:180132793-180133294 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:180133295-180133798 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16821 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:180142211-180142711 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:180208678-180209877 Neighboring gene RAD52 pseudogene 1

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_229364.1 

    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    179082752..179082921
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    179565954..179566123
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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