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LOC132090677 Neanderthal introgressed variant-containing enhancer experimental_6114 [ Homo sapiens (human) ]

Gene ID: 132090677, updated on 14-Oct-2023

Summary

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Gene symbol
LOC132090677
Gene description
Neanderthal introgressed variant-containing enhancer experimental_6114
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 1:232571969 or rs12035376 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132090677 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (232436138..232436307)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (231821720..231821889)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373196 Neighboring gene uncharacterized LOC105373198 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:232515217-232515718 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_5949 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_5966 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_5991 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_6018 Neighboring gene signal induced proliferation associated 1 like 2 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_6136 Neighboring gene NANOG hESC enhancer GRCh37_chr1:232603849-232604410 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_6156 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:232614076-232614278 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:232684300-232684923 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:232686883-232687411 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:232687412-232687939 Neighboring gene Sharpr-MPRA regulatory region 1023 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:232691629-232692200 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:232726700-232727200 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1957 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1958 Neighboring gene uncharacterized LOC124904551 Neighboring gene RNA, U6 small nuclear 1211, pseudogene

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

General gene information

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Other Names

  • emVar-containing allelic enhancer experimental_6114

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_231236.1 

    Range
    101..270
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    232436138..232436307
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    231821720..231821889
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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