rs10800447 (CCDC181/SLC19A2): NME7 eQTL Variant
Key takeaways
- rs10800447 sits near CCDC181 (coiled-coil domain containing 181) and SLC19A2, a gene that encodes a thiamine (vitamin B1) transporter.
- Carriers of the ALT allele consistently show higher NME7 gene expression across at least eight tissue types.
- Expression effects are among the strongest seen in GTEx data, with a p-value of 8.4e-36 in thyroid tissue.
- No direct disease associations for rs10800447 are established in the provided research literature.
- The downstream health consequences of increased NME7 expression from this variant have not been established.
Key takeaways
- rs10800447 sits near CCDC181 (coiled-coil domain containing 181) and SLC19A2, a gene that encodes a thiamine (vitamin B1) transporter.
- Carriers of the ALT allele (the non-reference version of the variant) consistently show higher NME7 gene expression across at least eight tissue types.
- Expression effects are among the strongest seen in GTEx data, with a p-value of 8.4e-36 in thyroid tissue (p-values indicate statistical confidence; lower numbers indicate stronger evidence).
- No direct disease associations for rs10800447 are established in the provided research literature.
- The downstream health consequences of increased NME7 expression from this variant have not been established.
What the research says GTEx v11 (953 donors), a large reference dataset that maps how genetic variants affect gene expression across human tissues, identifies rs10800447 as an eQTL -- a variant that influences how much of a specific gene is produced in a given tissue -- for NME7 across eight tissue types, with p-values ranging from 1.3e-14 to 8.4e-36 GTEx Portal. A genome-wide association study (GWAS) of Alzheimer's disease cognitive and imaging biomarkers, analyzing 565,373 single nucleotide polymorphisms (SNPs) across 1,576 participants in the Alzheimer's Disease Neuroimaging Initiative (ADNI), is included among the source materials for this locus, though the available study text does not report rs10800447 as a significant association.
Reported associations
- NME7 expression: The ALT allele is linked to increased expression of the NME7 gene across eight tissues -- EBV-transformed lymphocytes (p=1.3e-14), cultured fibroblasts (p=6.7e-31), thyroid (p=8.4e-36), sigmoid colon (p=1.5e-22), breast mammary tissue (p=1.2e-18), esophagus muscularis (p=6.2e-31), visceral omentum adipose (p=7.8e-20), and tibial artery (p=2.2e-26) GTEx Portal.
- Alzheimer's disease biomarkers (study context only): A GWAS of 565,373 SNPs across 1,576 ADNI participants covers the genomic region containing this locus and examined 16 cognitive and imaging measures, but does not report rs10800447 as a primary significant association in the text provided.
Evidence quality Expression-level evidence is robust: GTEx v11, drawing on 953 donors, reports NME7 eQTL associations at FDR (false discovery rate, a statistical threshold for controlling false positives) below 0.05 across all eight tissues, with p-values ranging from 1.3e-14 to 8.4e-36 GTEx Portal. Phenotypic disease association evidence is absent from the provided literature: the GWAS of Alzheimer's disease biomarkers (Lee B, Yao X, Shen L, BMC Genomics 2022), which analyzed 16 cognitive and imaging measures across 1,576 ADNI participants, identifies rs5011804 at 12p12.1 as its primary novel finding and does not identify this variant as a significant association in the text available. The clinical significance of the NME7 eQTL effect observed here is therefore currently unknown.
Tissue-specific expression effects
- NME7: The ALT allele is associated with increased expression across eight tissue types -- EBV-transformed lymphocytes, cultured fibroblasts, thyroid, sigmoid colon, breast mammary tissue, esophagus muscularis, visceral omentum adipose, and tibial artery. Thyroid and esophagus muscularis show effects at the high end of statistical confidence, with p-values below 1e-30 GTEx Portal.
Lifestyle considerations No lifestyle considerations on file for this variant.
Frequently asked questions
What genes are near rs10800447?
rs10800447 is located near two genes: CCDC181, which encodes a coiled-coil structural protein, and SLC19A2, which encodes a transporter that moves thiamine (vitamin B1) into cells.
What effect does rs10800447 have on gene expression?
The ALT allele of rs10800447 is associated with increased expression of the NME7 gene across eight tissue types, including thyroid, colon, breast mammary tissue, and cultured fibroblasts. This type of variant is called an expression quantitative trait locus, or eQTL.
Is rs10800447 linked to any disease?
Based on the provided research, no direct disease associations for rs10800447 have been established. A genome-wide association study of Alzheimer's disease biomarkers covers this genomic region but does not report rs10800447 as a significant finding in the available text.
What is an eQTL?
An eQTL, short for expression quantitative trait locus, is a genetic variant that influences how much of a specific gene is produced in a given tissue. rs10800447 functions as an eQTL for the NME7 gene in at least eight tissues.
What is SLC19A2?
SLC19A2 encodes a thiamine transporter, a protein that moves vitamin B1 into cells. It is one of the two genes flanking rs10800447, though the specific effect of this variant on SLC19A2 function is not established in the provided literature.