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LOC132090830 Neanderthal introgressed variant-containing enhancer experimental_11225 [ Homo sapiens (human) ]

Gene ID: 132090830, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132090830
Gene description
Neanderthal introgressed variant-containing enhancer experimental_11225
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 both the introgressed and non-introgressed 10:133892917 or rs6560679 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132090830 in Genome Data Viewer
Location:
chromosome: 10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (132079328..132079497)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (133019577..133019746)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (133892832..133893001)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene protein phosphatase 2 regulatory subunit Bdelta Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133785771-133786641 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:133794606-133795530 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2951 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2952 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:133809534-133810520 Neighboring gene uncharacterized LOC124902525 Neighboring gene BCL2 interacting protein 3 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:133820384-133820908 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:133823019-133823543 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133832958-133833629 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133842692-133843192 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133852590-133853427 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133857569-133858086 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133858087-133858604 Neighboring gene Janus kinase and microtubule interacting protein 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133878227-133878974 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:133881249-133881749 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_11218 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_11222 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_11227 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133920928-133921428 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133933330-133934168 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133934169-133935006 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:133951279-133951800 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:133955152-133955999 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:133956000-133956846 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133959409-133959910 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133959911-133960410 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133960832-133961794 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:133977007-133977706 Neighboring gene JAKMIP3 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:134001171-134001672 Neighboring gene dihydropyrimidinase like 4

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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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_11225

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_231389.1 

    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    132079328..132079497
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    133019577..133019746
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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