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LOC132090858 Neanderthal introgressed variant-containing enhancer experimental_24566 [ Homo sapiens (human) ]

Gene ID: 132090858, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132090858
Gene description
Neanderthal introgressed variant-containing enhancer experimental_24566
Gene type
biological region
Feature type(s)
regulatory: enhancer, transcriptional_cis_regulatory_region
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 expression-modulating variant (emVar), and was validated as a functional enhancer by massively parallel reporter assays (MPRAs) in K562 erythroleukemia cells, with activity observed for the non-introgressed 12:113442257 or rs1293749 variant allele. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132090858 in Genome Data Viewer
Location:
chromosome: 12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (113004367..113004536)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (112980990..112981159)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (113442172..113442341)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7052 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24142 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_24146 and experimental_24152 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24159 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24163 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_24171 and experimental_24176 Neighboring gene 2'-5'-oligoadenylate synthetase 1 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_24215 and experimental_24231 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_24264 and experimental_24270 Neighboring gene Sharpr-MPRA regulatory region 3381 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_24293 and experimental_24295 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_24298, experimental_24301 and experimental_24306 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_24317/24320 and experimental_24338 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_24357 and experimental_24368 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24404 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24448 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_24456 and experimental_24461 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24463 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24487 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7053 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24505 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24515 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4887 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24520 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24535 Neighboring gene MPRA-validated peak1965 silencer Neighboring gene 2'-5'-oligoadenylate synthetase 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:113400746-113401246 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:113401247-113401747 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24547 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24553 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7054 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7056 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7055 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7057 Neighboring gene 2'-5'-oligoadenylate synthetase 2 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24560 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24567 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:113444541-113445740 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24568 Neighboring gene inner mitochondrial membrane peptidase subunit 1 pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4888 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7058 Neighboring gene ribosomal protein S15a pseudogene 32

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)

General gene information

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Other Names

  • emVar-containing allelic enhancer experimental_24566

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_231417.1 

    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    113004367..113004536
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    112980990..112981159
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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