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LOC132090642 Neanderthal introgressed variant-containing enhancer experimental_63138 [ Homo sapiens (human) ]

Gene ID: 132090642, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132090642
Gene description
Neanderthal introgressed variant-containing enhancer experimental_63138
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 22:25519885 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132090642 in Genome Data Viewer
Location:
chromosome: 22
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (25123833..25124002)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (25585111..25585280)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (25519800..25519969)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 9438 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13557 Neighboring gene LHFPL tetraspan subfamily member 7 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:25354355-25354854 Neighboring gene KIAA1671 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:25365545-25366128 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:25390751-25391348 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:25398411-25398910 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr22:25421915-25423114 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:25457216-25458130 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:25462486-25463045 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:25465590-25466140 Neighboring gene Sharpr-MPRA regulatory region 10625 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:25494863-25495382 Neighboring gene KIAA1671 antisense RNA 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:25506614-25507476 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:25507477-25508338 Neighboring gene Sharpr-MPRA regulatory region 2564 Neighboring gene Sharpr-MPRA regulatory region 1539 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_63172 Neighboring gene STMN3 pseudogene 1 Neighboring gene crystallin beta B3

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)

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_231200.1 

    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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    25123833..25124002
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    25585111..25585280
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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