U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC132089310 Neanderthal introgressed variant-containing enhancer experimental_87727 [ Homo sapiens (human) ]

Gene ID: 132089310, updated on 12-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC132089310
Gene description
Neanderthal introgressed variant-containing enhancer experimental_87727
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 the non-introgressed 6:111845573 variant allele. [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 LOC132089310 in Genome Data Viewer
Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (111524285..111524454)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (112707283..112707452)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (111845488..111845657)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene REV3 like, DNA directed polymerase zeta catalytic subunit Neighboring gene ReSE screen-validated silencer GRCh37_chr6:111751696-111751904 Neighboring gene MPRA-validated peak6035 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24943 Neighboring gene bromodomain containing 7 pseudogene 4 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:111798355-111799247 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:111799845-111800569 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24944 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17475 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17476 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17477 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17478 Neighboring gene TRAF3IP2 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17479 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24945 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24946 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24947 Neighboring gene uncharacterized LOC107986520 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:111828147-111828670 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:111828671-111829193 Neighboring gene uncharacterized LOC107986522 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:111861530-111861704 Neighboring gene VISTA enhancer hs1690 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:111880567-111881066 Neighboring gene MPRA-validated peak6037 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:111885602-111886274 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:111886439-111887638 Neighboring gene TRAF3 interacting protein 2 Neighboring gene TRAF3IP2 eExon liver enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24949

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)

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_229869.1 

    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    111524285..111524454
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    112707283..112707452
    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