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LOC132205954 Neanderthal introgressed variant-containing enhancers experimental_58196 and experimental_58198 [ Homo sapiens (human) ]

Gene ID: 132205954, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132205954
Gene description
Neanderthal introgressed variant-containing enhancers experimental_58196 and experimental_58198
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 includes two overlapping subregions containing Neanderthal adaptively introgressed genetic variants, with one having an expression-modulating variant (emVar). Both subregions were validated as enhancers by massively parallel reporter assays (MPRAs) in K562 erythroleukemia cells, with activity observed for the introgressed 2:242930000 or rs117441917 variant allele for one subregion, and for the non-introgressed 2:242930040 variant allele for the other subregion. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132205954 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 (241987764..241987973)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (242496438..242496647)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (242929915..242930124)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1237 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:242842086-242842730 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:242842731-242843374 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:242843375-242844020 Neighboring gene family with sequence similarity 240 member C Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:242884151-242884650 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:242892163-242892811 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:242892812-242893459 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:242907927-242908434 Neighboring gene long intergenic non-protein coding RNA 1238 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:242927157-242927693 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:242946994-242947615 Neighboring gene uncharacterized FLJ38379 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:242975433-242975936 Neighboring gene uncharacterized LOC105373980

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 Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • Neanderthal introgressed variant-containing enhancer experimental_58196
  • Neanderthal introgressed variant-containing enhancer experimental_58198
  • emVar-containing allelic enhancer experimental_58196

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_231487.1 

    Range
    101..310
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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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    241987764..241987973
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_187523.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    26459..26668
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

  1. NT_187647.1 Reference GRCh38.p14 ALT_REF_LOCI_2

    Range
    26459..26668
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    242496438..242496647
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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