U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC132090901 Neanderthal introgressed variant-containing enhancer experimental_50709 [ Homo sapiens (human) ]

Gene ID: 132090901, updated on 12-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC132090901
Gene description
Neanderthal introgressed variant-containing enhancer experimental_50709
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 18:77507495 or rs56378884 variant alleles. [provided by RefSeq, Sep 2023]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See LOC132090901 in Genome Data Viewer
Location:
chromosome: 18
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (79747410..79747579)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (80022651..80022820)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (77507410..77507579)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:77371029-77371622 Neighboring gene uncharacterized LOC105372228 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:77371623-77372215 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr18:77378514-77379195 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr18:77379196-77379876 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:77386241-77386740 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:77386889-77387390 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:77390729-77391230 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:77404966-77405480 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:77417519-77418054 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:77416983-77417518 Neighboring gene CTDP1 divergent transcript Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:77438928-77439435 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:77439436-77439944 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:77441560-77442068 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:77442069-77442575 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:77457803-77458304 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:77458305-77458804 Neighboring gene CTD phosphatase subunit 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:77471187-77471379 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:77557221-77557817 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:77576519-77577020 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:77577021-77577520 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13545 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr18:77585975-77587174 Neighboring gene potassium voltage-gated channel modifier subfamily G member 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:77601626-77602126 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9578 Neighboring gene Sharpr-MPRA regulatory region 1017 Neighboring gene Sharpr-MPRA regulatory region 1467 Neighboring gene Sharpr-MPRA regulatory region 11655 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:77664167-77664802 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:77672372-77673288 Neighboring gene solute carrier family 66 member 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9579 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9580 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9581 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9582

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

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

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

Go to the top of the page Help

Other Names

  • emVar-containing allelic enhancer experimental_50709

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_231460.1 

    Range
    101..270
    Download
    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_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    79747410..79747579
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    80022651..80022820
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases