rs12740374

Chromosome : 1 , Position: 109274968

Most conditions are affected by anywhere from hundreds to millions of genetic variants (SNPs). A single SNP usually has a minor contribution to a person’s overall genetic risk for a certain condition. That is why you shouldn't consider or act on a SNP in isolation. Instead, we use SNPs to determine polygenic risk scores (PRSs), which are the basis of most health reports.

Reference Allele: G

Alternative Alleles: T

Associated Genes

SORT1

CELSR2

PSRC1

ELAPOR1

SARS1

CYB561D1

GSTM4

GPR61

GSTM3

AMIGO1

SYPL2

GNAI3

GSTM1

MYBPHL

C1ORF194

PSMA5

AMPD2

ATXN7L2

TAF13

TMEM167B

WDR47

AKNAD1

CLCC1

GNAT2

GPSM2

GSTM2

GSTM5

EPS8L3

Traits

Trait	Variant	PMID	Author (year)
Total cholesterol levels	T	Sci Rep	Moon S (2019)
Lipoprotein phospholipase A2 activity in cardiovascular disease	T	PLoS One	Yeo A (2017)
Blood protein levels [GRN]	T	Nat Commun	Yao C (2018)
Low density lipoprotein cholesterol levels [AA]	T	Nat Genet	Hoffmann TJ (2018)
Low density lipoprotein cholesterol levels [Hispanic]	T	Nat Genet	Hoffmann TJ (2018)
Total cholesterol levels [AA]	T	Nat Genet	Hoffmann TJ (2018)
Total cholesterol levels [Hispanic]	T	Nat Genet	Hoffmann TJ (2018)
LDL cholesterol	T	Nat Genet	Willer CJ (2013)
Medication use (HMG CoA reductase inhibitors)	T	Nat Commun	Wu Y (2019)
Cholesterol, total	T	Genome Med	Nagy R (2017)
E-selectin levels	T	Nat Metab	Folkersen L (2020)
Medication use (antithrombotic agents)	T	Nat Commun	Wu Y (2019)
Apolipoprotein A1 levels	T	PLoS Med	Richardson TG (2020)
Lipoprotein-associated phospholipase A2 activity and mass [activity]	T	Circ Cardiovasc Genet	Chu AY (2012)
HDL cholesterol	T	Nat Genet	Willer CJ (2013)
HDL cholesterol levels	T	PLoS Med	Richardson TG (2020)
Mean spheric corpuscular volume	T	Cell	Vuckovic D (2020)
Cardiovascular disease	T	Am J Hum Genet	Kichaev G (2018)
Cholesterol lowering medication \| medication for cholesterol, blood pressure or diabetes	T	Unknown journal	UKB Neale v2 (2018)
Coronary artery bypass grafting (no controls excluded)	T	Unknown journal	FINNGEN_R5 (2021)
Coronary artery disease	T	Nat Genet	Koyama S (2020)
Disorders of lipoid metabolism	T	Unknown journal	UKB SAIGE (2018)
Ezetimibe \| treatment/medication code	T	Unknown journal	UKB Neale v2 (2018)
HDL cholesterol levels x long total sleep time interaction (2df test)	T	Nat Commun	Noordam R (2019)
Height	T	Am J Hum Genet	Kichaev G (2018)
High cholesterol \| non-cancer illness code, self-reported	T	Unknown journal	UKB Neale v2 (2018)
Hyperlipidemia	T	Unknown journal	UKB SAIGE (2018)
Ischemic heart disease	T	Unknown journal	UKB SAIGE (2018)
LDL cholesterol levels	T	Genet Epidemiol	Han S (2019)
LDL cholesterol levels x long total sleep time interaction (2df test)	T	Nat Commun	Noordam R (2019)
Low density lipoprotein cholesterol levels	T	PLoS One	Andaleon A (2019)
Myocardial infarction	T	Eur Heart J	Hartiala JA (2021)
None of the above \| medication for cholesterol, blood pressure or diabetes	T	Unknown journal	UKB Neale v2 (2018)
Serum total cholesterol levels	T	PLoS Genet	Davis JP (2017)
Simvastatin \| treatment/medication code	T	Unknown journal	UKB Neale v2 (2018)
Total cholesterol levels in LDL	T	PLoS Genet	Davis JP (2017)

Summary

Pharmacogenetic meta-analysis of genome-wide association studies of LDL cholesterol response to statins found each minor allele to increase statin effectiveness by 1.3% (rs646776, β=−0.013, s.e.=0.002, P=1.05 × 10−9 and rs12740374, β=−0.013, s.e.=0.002, P=1.05 × 10−9).

[PMID 20686566] From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus

[PMID 22539988] Evaluation of the Metabochip Genotyping Array in African Americans and Implications for Fine Mapping of GWAS-Identified Loci: The PAGE Study

[PMID 18262040] LDL-cholesterol concentrations: a genome-wide association study.

[PMID 19299407] Replication of genetic associations with plasma lipoprotein traits in a multiethnic sample.

[PMID 19822575] Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing.

[PMID 19913121] Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.

[PMID 19951432] Analysis of recently identified dyslipidemia alleles reveals two loci that contribute to risk for carotid artery disease.

[PMID 24059109] [Association between SNP rs12740374 and acute ischemic stroke in Chinese Han population]

[PMID 23723249] GWAS3D: Detecting human regulatory variants by integrative analysis of genome-wide associations, chromosome interactions and histone modifications.

[PMID 24922790] 214 Generation of Isogenic Cell Lines to Study a Single Disease Associated Variant at the 1P13 Cad Risk Locus

Population Alleles Frequency

ethhicity	frequency
African/African-American	0.2536
Latino/Admixed American	0.1797
Ashkenazi Jewish	0.1862
East Asian	0.0611
European	0.2203
Other (population not assigned)	0.2155

Frequently Asked Questions

Why Are Alleles for This SNP Different Elsewhere? Major vs. Reference Allele Is My Variant Good or Bad? SNP vs. Mutation

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