NyuWa Chinese Population Variant Database

Basic
Region Annotation
Population
xQTL
Linkage disequilibrium
GWAS Catalog
Epigenetic signals

Variant: 20-37359581-STR-8AAAC4

START:	37359581
END:	37359588
Repeat motif:	AAAC
PERIOD:	4
Type:	STR
Ref Length:	8
Alt Length:	4
Allele Count:	1881
Allele Number:	20896
Allele Frequency:	0.09
Number of Homozygotes:	102
Ref Sequence:	AACAAACA
Alt Sequence:	AACA

Reference: T2T-CHM13

T2T-specific: not in

Browser:

Region annotation

	Region	Gene ID	Gene Detail
RefSeq	intronic	CPNE1	.

Allele frequency distribution

Population TR length distribution

Ref allele length = 8

xQTL Plot

xQTL results for 20-37359581-STR-8AAAC4

Linkage disequilibrium Plot

LD results for 20-37359581-STR-8AAAC4

The R² statistic is the correlation coefficient of genotypes between pairs of loci. D' is the normalized LD statistic by dividing LD statistic D by its theoretical maximum, while D = p_AB - p_A * p_B.

GWAS Catalog

LD SNP	LD R2	Risk Allele	Gene	Trait Class	Trait	OR/Beta	P-value	Study	Ancestry
20-37386709-C-G	AFR:0.27 AMR:0.89 EAS:1.00 EUR:0.99 SAS:0.98 10K:0.80	rs113203744-G		Cancer	Basal cell carcinoma	0.9329	3E-9	GCST90328134	European, Hispanic or Latin American
20-37560638-G-A	AFR:0.63 AMR:0.87 EAS:0.99 EUR:0.80 SAS:0.79 10K:0.86	rs11697087-?	PFH20	Cardiovascular disease	Cardioembolic stroke (CCS and TOAST classification)	1.26	3E-9	GCST010164	African unspecified, European, European, NR
20-37381187-T-C	AFR: AMR:0.74 EAS:1.00 EUR:0.68 SAS:0.95 10K:0.71	rs11698796-T		Lipid or lipoprotein measurement	Triglyceride levels in IDL	0.0335314	3E-8	GCST90092841	European
20-37381187-T-C	AFR: AMR:0.74 EAS:1.00 EUR:0.68 SAS:0.95 10K:0.71	rs11698796-T		Lipid or lipoprotein measurement	Phospholipid levels in very small VLDL	0.0354145	5E-9	GCST90093036	European
20-37381187-T-C	AFR: AMR:0.74 EAS:1.00 EUR:0.68 SAS:0.95 10K:0.71	rs11698796-T		Lipid or lipoprotein measurement	Total lipid levels in very small VLDL	0.0345407	1E-8	GCST90093034	European
20-37334869-C-A	AFR:0.28 AMR:0.62 EAS:0.86 EUR:0.55 SAS:0.83 10K:0.64	rs11699996-?		Other measurement	Multi-trait sex score		1E-11	GCST90270118	European
20-37516687-A-G	AFR:0.30 AMR:0.76 EAS:0.61 EUR:0.65 SAS:0.81 10K:0.62	rs11906854-G	intergenic	Cardiovascular disease	Migraine - clinic-based	1.17	7E-6	GCST002079	European
20-37367854-A-G	AFR:0.31 AMR:0.89 EAS:1.00 EUR:1.00 SAS:0.98 10K:0.84	rs12480408-G	NR	Hematological measurement	Lymphocyte count		1E-11	GCST90002320	African American or Afro-Caribbean, African unspecified, European, East Asian, Hispanic or Latin American, South Asian
20-37351727-G-C	AFR:0.30 AMR:0.90 EAS:0.97 EUR:0.99 SAS:0.98 10K:0.82	rs12481228-C		Other measurement	Copine-1 levels (CPNE1.5346.24.3)	0.98	2E-146	GCST90240791	European
20-37333026-G-A	AFR:0.28 AMR:0.86 EAS:0.97 EUR:0.98 SAS:0.96 10K:0.81	rs143646210-A		Other measurement	Serum levels of protein CPNE1	1.02484	2E-295	GCST90089009	European
20-37440819-G-C	AFR: AMR:0.72 EAS:0.61 EUR:0.69 SAS:0.92 10K:0.59	rs2378392-C		Lipid or lipoprotein measurement	Free cholesterol in IDL	0.0364	2E-9	GCST90301979	East Asian, South Asian, European
20-37483731-C-T	AFR:0.36 AMR:0.90 EAS:0.61 EUR:0.93 SAS:0.85 10K:0.68	rs2425143-T		Other measurement	Copine-1 levels	1.206	4E-73	GCST90100879	European
20-37423334-A-G	AFR:0.81 AMR:1.00 EAS:0.66 EUR:1.00 SAS:0.98 10K:0.78	rs6058303-?	NR	Other measurement	Protein quantitative trait loci		1E-11	GCST010900	European
20-37423334-A-G	AFR:0.81 AMR:1.00 EAS:0.66 EUR:1.00 SAS:0.98 10K:0.78	rs6058303-?	NR	Other measurement	Protein quantitative trait loci		1E-11	GCST010900	European
20-37500344-A-G	AFR:0.23 AMR:0.73 EAS:0.58 EUR:0.65 SAS:0.81 10K:0.59	rs6058322-A		Lipid or lipoprotein measurement	Phospholipids in very small VLDL	0.0358	3E-10	GCST90302158	East Asian, South Asian, European
20-37500344-A-G	AFR:0.23 AMR:0.73 EAS:0.58 EUR:0.65 SAS:0.81 10K:0.59	rs6058322-G		Body measurement	Height	0.03215	9E-21	GCST90245846	African unspecified
20-37354209-G-T	AFR:0.87 AMR:1.00 EAS:0.99 EUR:0.99 SAS:1.00 10K:0.95	rs6060524-T		Other measurement	Copine-1 levels	1.233	4E-988	GCST90247129	European
20-37394179-C-T	AFR:0.27 AMR:0.89 EAS:1.00 EUR:1.00 SAS:0.98 10K:0.80	rs6060547-?		Other measurement	Copine-1 levels	1.02	9E-149	GCST90137861	African American or Afro-Caribbean
20-37438499-C-T	AFR:0.83 AMR:1.00 EAS:1.00 EUR:1.00 SAS:0.98 10K:0.96	rs6060578-C	CPNE1	Other measurement	Blood protein levels	1.0387857	5E-157	GCST006585	European
20-37566982-T-C	AFR:0.63 AMR:0.97 EAS:0.99 EUR:0.69 SAS:0.72 10K:0.84	rs6060637-?		Other measurement	Multi-trait sex score		8E-13	GCST90270118	European
20-37345205-G-A	AFR:0.30 AMR:0.90 EAS:0.97 EUR:1.00 SAS:1.00 10K:0.82	rs61016611-A		Body measurement	Height	0.062	1E-10	GCST90131910	East Asian
20-37390337-G-T	AFR:0.27 AMR:0.89 EAS:1.00 EUR:0.99 SAS:0.98 10K:0.80	rs7267759-T	NR	Hematological measurement	Lymphocyte count	0.022555	9E-13	GCST90002316	European
20-37390337-G-T	AFR:0.27 AMR:0.89 EAS:1.00 EUR:0.99 SAS:0.98 10K:0.80	rs7267759-T	RP1-309K20.6, NFS1	Body measurement	Hip circumference adjusted for BMI	0.0412937	1E-15	GCST012227	European
20-37483371-T-C	AFR:0.42 AMR:0.95 EAS:0.99 EUR:0.93 SAS:0.85 10K:0.84	rs7273174-C		Hematological measurement	Lymphocyte percentage of white cells	0.02232549	4E-10	GCST90002389	European
20-37353044-A-C	AFR:0.44 AMR:0.81 EAS:0.97 EUR:0.68 SAS:0.95 10K:0.81	rs78084033-A	NR	Biological process	Intelligence	5.649	2E-8	GCST006250	European

Epigenetic signals

Marker	Cell type	Range
H3K36me3	RWPE2	37343058-37359760
H3K4me1	HAP-1	37359316-37361517

Fixation index Rst

The Fixation index Rst was adopted as the measure for assessing population differences in tandem repeat variation.

NyuWa Global 10K T2T Variant Database

Variant Database and Imputation service with world population genome resource

Variant: 20-37359581-STR-8AAAC4

Reference: T2T-CHM13

T2T-specific: not in

Browser:

Ref allele length = 8

xQTL results for 20-37359581-STR-8AAAC4

LD results for 20-37359581-STR-8AAAC4

NyuWa Global 10K T2T Variant Database

Variant Database and Imputation service with world population genome resource

Variant: 20-37359581-STR-8AAAC4

Reference: T2T-CHM13 T2T-specific: not in

Browser: Browser

Ref allele length = 8

xQTL results for 20-37359581-STR-8AAAC4

LD results for 20-37359581-STR-8AAAC4

Reference: T2T-CHM13

T2T-specific: not in

Browser: