NyuWa Chinese Population Variant Database

Basic
Region Annotation
Population
xQTL
Linkage disequilibrium
GWAS Catalog
Epigenetic signals

Variant: 6-32478685-MEI-SVA

Allele Count:	737
Allele Number:	19320
Allele Frequency:	0.0381
SVTYPE:	Retroposon/SVA
MEI:	SVA_F
START (0-based):	32478685
END (0-based):	32478733
SVLEN:	590
MESTRAND:	-
Number of Homozygotes:	44

Reference: T2T-CHM13

T2T-specific: 6:32472837-32480832

Browser:

Region annotation

	Region	Gene ID	Gene Detail
RefSeq	intergenic	HLA-DQA1;HLA-DQB1	dist=5920;dist=3759

Allele frequency distribution

xQTL Plot

xQTL results for 6-32478685-MEI-SVA

Linkage Disequilibrium Plot

LD results for 6-32478685-MEI-SVA

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
6-32435139-C-T	AFR:0.28 AMR:0.21 EAS:0.62 EUR:0.22 SAS:0.93 10K:0.57	rs144123929-C		Lipid or lipoprotein measurement	Cholesteryl esters to total lipids ratio in IDL	0.0862226	1E-8	GCST90092834	European
6-32523760-C-T	AFR:0.84 AMR:0.46 EAS:0.58 EUR:0.90 SAS:0.94 10K:0.70	rs1613056-?		Immune system disorder	Hypothyroidism or rheumatoid arthritis (pleiotropy)		3E-99	GCST90428109	European
6-32528694-C-A	AFR:0.84 AMR:0.46 EAS:0.58 EUR:0.92 SAS:0.94 10K:0.72	rs1617322-?		Immune system disorder	Hypothyroidism or rheumatoid arthritis (pleiotropy)		3E-98	GCST90428109	European
6-32523477-G-A	AFR:0.84 AMR:0.46 EAS:0.58 EUR:0.92 SAS:0.94 10K:0.70	rs1794277-?		Other measurement	Seropositivity for streptococcus pneumoniae peptide (agilent_223208)	10.148	3E-24	GCST90295773	NR
6-32523477-G-A	AFR:0.84 AMR:0.46 EAS:0.58 EUR:0.92 SAS:0.94 10K:0.70	rs1794277-?		Immune system disorder	Hypothyroidism or rheumatoid arthritis (pleiotropy)		3E-99	GCST90428109	European
6-32522006-A-T	AFR:0.84 AMR:0.46 EAS:0.58 EUR:0.92 SAS:0.94 10K:0.72	rs1794280-T	NR	Other measurement	Anti-sp100 seropositivity in primary biliary cholangitis	3.89	6E-28	GCST007737	East Asian
6-32522006-A-T	AFR:0.84 AMR:0.46 EAS:0.58 EUR:0.92 SAS:0.94 10K:0.72	rs1794280-T		Other disease	Hyperthyroidism	0.5463	2E-44	GCST90018860	European, East Asian
6-32522006-A-T	AFR:0.84 AMR:0.46 EAS:0.58 EUR:0.92 SAS:0.94 10K:0.72	rs1794280-?		Immune system disorder	Hypothyroidism or rheumatoid arthritis (pleiotropy)		1E-101	GCST90428109	European
6-32521193-C-T	AFR:0.84 AMR:0.46 EAS:0.58 EUR:0.92 SAS:0.94 10K:0.73	rs1794283-?		Immune system disorder	Hypothyroidism or rheumatoid arthritis (pleiotropy)		4E-101	GCST90428109	European
6-32526012-T-G	AFR:0.84 AMR:0.46 EAS:0.58 EUR:0.92 SAS:0.94 10K:0.72	rs1794511-G		Other measurement	IgD on IgD+ CD24+ B cell	0.2439	7E-13	GCST90001820	European
6-32526012-T-G	AFR:0.84 AMR:0.46 EAS:0.58 EUR:0.92 SAS:0.94 10K:0.72	rs1794511-T		Other trait	Amiloride-sensitive amine oxidase [copper-containing] levels	0.132	9E-12	GCST90246408	European
6-32526012-T-G	AFR:0.84 AMR:0.46 EAS:0.58 EUR:0.92 SAS:0.94 10K:0.72	rs1794511-?		Immune system disorder	Hypothyroidism or rheumatoid arthritis (pleiotropy)		7E-99	GCST90428109	European
6-32517298-A-C	AFR:0.84 AMR:0.46 EAS:0.58 EUR:0.90 SAS:0.94 10K:0.70	rs1794519-?		Immune system disorder	Hypothyroidism or rheumatoid arthritis (pleiotropy)		1E-100	GCST90428109	European
6-32526605-T-G	AFR:0.84 AMR:0.46 EAS:0.58 EUR:0.92 SAS:0.94 10K:0.72	rs1794530-?		Immune system disorder	Hypothyroidism or rheumatoid arthritis (pleiotropy)		2E-99	GCST90428109	European
6-32522723-G-A	AFR:0.84 AMR:0.46 EAS:0.58 EUR:0.92 SAS:0.94 10K:0.72	rs2647044-A	BRD2, BTNL2, C6orf10, HCG23, HLA-DMA, HLA-DMB, HLA-DOA, HLA-DOB, HLA-DPA1, HLA-DQA1, HLA-DQA2, HLA-DQB1, HLA-DQB2, HLA-DRA, HLA-DRB1, HLA-DRB5, HLA-DRB6, LOC100294145, NOTCH4, PSMB8, PSMB9, TAP1, TAP2, TAPSAR1	Other disease	Asthma	1.1522182	4E-15	GCST008916	European
6-32522723-G-A	AFR:0.84 AMR:0.46 EAS:0.58 EUR:0.92 SAS:0.94 10K:0.72	rs2647044-A	HLA-DRB1	Immune system disorder	Type 1 diabetes	8.3	1E-16	GCST000054	European
6-32522723-G-A	AFR:0.84 AMR:0.46 EAS:0.58 EUR:0.92 SAS:0.94 10K:0.72	rs2647044-G	HLA-DQB1	Other measurement	Pulmonary function	0.044	6E-6	GCST001248	European
6-32522723-G-A	AFR:0.84 AMR:0.46 EAS:0.58 EUR:0.92 SAS:0.94 10K:0.72	rs2647044-?		Other measurement	Seropositivity for staphylococcus aureus peptide (agilent_226247)	8.569	1E-17	GCST90295547	NR
6-32522723-G-A	AFR:0.84 AMR:0.46 EAS:0.58 EUR:0.92 SAS:0.94 10K:0.72	rs2647044-?		Other measurement	Seropositivity for staphylococcus aureus peptide (agilent_222381)	9.68	4E-22	GCST90295549	NR
6-32522723-G-A	AFR:0.84 AMR:0.46 EAS:0.58 EUR:0.92 SAS:0.94 10K:0.72	rs2647044-?		Other measurement	Seropositivity for staphylococcus aureus peptide (agilent_236333)	8.91	5E-19	GCST90295552	NR
6-32522723-G-A	AFR:0.84 AMR:0.46 EAS:0.58 EUR:0.92 SAS:0.94 10K:0.72	rs2647044-?		Other measurement	Seropositivity for staphylococcaceae peptide (agilent_4825)	9.322	1E-20	GCST90295458	NR
6-32513786-A-G	AFR:0.84 AMR:0.46 EAS:0.58 EUR:0.92 SAS:0.94 10K:0.72	rs2856674-A	BRD2	Other measurement	Feeling nervous	6.41	2E-10	GCST006948	European
6-32513786-A-G	AFR:0.84 AMR:0.46 EAS:0.58 EUR:0.92 SAS:0.94 10K:0.72	rs2856674-?	HLA-DQA	Digestive system disorder	Primary sclerosing cholangitis		1E-6	GCST006670	European
6-32513786-A-G	AFR:0.84 AMR:0.46 EAS:0.58 EUR:0.92 SAS:0.94 10K:0.72	rs2856674-G	MTCO3P1	Body measurement	A body shape index	0.0297899	7E-14	GCST90020024	European
6-32513786-A-G	AFR:0.84 AMR:0.46 EAS:0.58 EUR:0.92 SAS:0.94 10K:0.72	rs2856674-G		Hematological measurement	Hemoglobin concentration	0.05117	1E-22	GCST90258652	European
6-32499706-T-C	AFR:0.84 AMR:0.46 EAS:0.60 EUR:0.92 SAS:0.94 10K:0.70	rs3104361-T	HLA-DQB1	Other measurement	Helicobacter pylori OMP antibody levels	0.18	7E-10	GCST90006914	European
6-32511584-T-C	AFR:0.84 AMR:0.46 EAS:0.58 EUR:0.92 SAS:0.94 10K:0.72	rs3129716-?	HLA-DQB1	Immune system disorder	Systemic lupus erythematosus		4E-9	GCST003103	European
6-32511584-T-C	AFR:0.84 AMR:0.46 EAS:0.58 EUR:0.92 SAS:0.94 10K:0.72	rs3129716-?		Other measurement	FAM3B/GUCA2A protein level ratio	0.166109	9E-66	GCST90314779	European
6-32511584-T-C	AFR:0.84 AMR:0.46 EAS:0.58 EUR:0.92 SAS:0.94 10K:0.72	rs3129716-?		Other measurement	HAVCR2/PILRA protein level ratio	0.0835696	3E-18	GCST90315028	European
6-32511584-T-C	AFR:0.84 AMR:0.46 EAS:0.58 EUR:0.92 SAS:0.94 10K:0.72	rs3129716-?		Other measurement	HAVCR2/TNFRSF1B protein level ratio	0.204194	1E-102	GCST90315030	European
6-32511584-T-C	AFR:0.84 AMR:0.46 EAS:0.58 EUR:0.92 SAS:0.94 10K:0.72	rs3129716-?		Other measurement	ITGA5/VCAM1 protein level ratio	0.110806	4E-30	GCST90315206	European
6-32511584-T-C	AFR:0.84 AMR:0.46 EAS:0.58 EUR:0.92 SAS:0.94 10K:0.72	rs3129716-?		Other measurement	FOLR2/HAVCR2 protein level ratio	0.165053	3E-69	GCST90314865	European
6-32511584-T-C	AFR:0.84 AMR:0.46 EAS:0.58 EUR:0.92 SAS:0.94 10K:0.72	rs3129716-?		Other measurement	CD300C/HAVCR2 protein level ratio	0.103823	2E-27	GCST90313789	European
6-32511584-T-C	AFR:0.84 AMR:0.46 EAS:0.58 EUR:0.92 SAS:0.94 10K:0.72	rs3129716-?		Other measurement	CDCP1/MSR1 protein level ratio	0.140893	4E-50	GCST90313938	European
6-32511584-T-C	AFR:0.84 AMR:0.46 EAS:0.58 EUR:0.92 SAS:0.94 10K:0.72	rs3129716-?		Other measurement	QPCT/RNASET2 protein level ratio	0.336381	9E-274	GCST90315758	European
6-32511584-T-C	AFR:0.84 AMR:0.46 EAS:0.58 EUR:0.92 SAS:0.94 10K:0.72	rs3129716-?		Other measurement	ROBO2/SCARF2 protein level ratio	0.0777629	4E-19	GCST90315784	European
6-32511584-T-C	AFR:0.84 AMR:0.46 EAS:0.58 EUR:0.92 SAS:0.94 10K:0.72	rs3129716-?		Other measurement	PLAUR/TREM2 protein level ratio	0.101906	2E-27	GCST90315676	European
6-32511584-T-C	AFR:0.84 AMR:0.46 EAS:0.58 EUR:0.92 SAS:0.94 10K:0.72	rs3129716-?		Other measurement	EFNA1/TNFRSF1A protein level ratio	0.11086	8E-33	GCST90314599	European
6-32511584-T-C	AFR:0.84 AMR:0.46 EAS:0.58 EUR:0.92 SAS:0.94 10K:0.72	rs3129716-?		Other measurement	IGSF8/NECTIN2 protein level ratio	0.115734	1E-33	GCST90315140	European
6-32511584-T-C	AFR:0.84 AMR:0.46 EAS:0.58 EUR:0.92 SAS:0.94 10K:0.72	rs3129716-?		Other measurement	PIK3IP1/TNFRSF1A protein level ratio	0.128004	3E-40	GCST90315653	European
6-32511584-T-C	AFR:0.84 AMR:0.46 EAS:0.58 EUR:0.92 SAS:0.94 10K:0.72	rs3129716-?		Other measurement	ADA2/COMP protein level ratio	0.181174	2E-80	GCST90313166	European
6-32511584-T-C	AFR:0.84 AMR:0.46 EAS:0.58 EUR:0.92 SAS:0.94 10K:0.72	rs3129716-?		Other measurement	ADGRE2/SIGLEC1 protein level ratio	0.0933404	3E-22	GCST90313178	European
6-32511584-T-C	AFR:0.84 AMR:0.46 EAS:0.58 EUR:0.92 SAS:0.94 10K:0.72	rs3129716-?		Neurological disorder	Polymyositis	2.65	2E-54	GCST90270217	European
6-32501585-A-C	AFR:0.84 AMR:0.46 EAS:0.60 EUR:0.92 SAS:0.94 10K:0.70	rs3134971-C		Other trait	Coiled-coil domain-containing protein 134 level in Chronic kidney disease with hypertension and no diabetes (15300_66)	0.93	1E-21	GCST90234306	African American or Afro-Caribbean
6-32499069-G-T	AFR:0.84 AMR:0.46 EAS:0.62 EUR:0.92 SAS:0.94 10K:0.71	rs3134977-?		Other measurement	Seropositivity for staphylococcus aureus peptide (twist_46764)	7.175	7E-13	GCST90295470	NR
6-32498901-A-T	AFR:0.84 AMR:0.46 EAS:0.62 EUR:0.92 SAS:0.94 10K:0.71	rs3134978-A		Other measurement	GDNF family receptor alpha-1 levels	0.17	8E-20	GCST90247719	European
6-32536438-C-T	AFR:0.74 AMR:0.38 EAS:0.56 EUR:0.57 SAS:0.88 10K:0.65	rs3957147-T	NR	Immune system disorder	Autoimmune traits	1.34	9E-9	GCST011008	European
6-32536438-C-T	AFR:0.74 AMR:0.38 EAS:0.56 EUR:0.57 SAS:0.88 10K:0.65	rs3957147-?		Other measurement	Seropositivity for streptococcus pneumoniae peptide (agilent_220951)	5.855	5E-9	GCST90295790	NR
6-32536438-C-T	AFR:0.74 AMR:0.38 EAS:0.56 EUR:0.57 SAS:0.88 10K:0.65	rs3957147-?		Other measurement	Seropositivity for streptococcus pneumoniae peptide (agilent_220944)	6.256	4E-10	GCST90295776	NR
6-32536438-C-T	AFR:0.74 AMR:0.38 EAS:0.56 EUR:0.57 SAS:0.88 10K:0.65	rs3957147-?		Other measurement	Seropositivity for streptococcus pneumoniae peptide (agilent_220184)	6.418	1E-10	GCST90295777	NR
6-32536438-C-T	AFR:0.74 AMR:0.38 EAS:0.56 EUR:0.57 SAS:0.88 10K:0.65	rs3957147-?		Other measurement	Seropositivity for streptococcus pneumoniae peptide (agilent_231039)	5.622	2E-8	GCST90295781	NR
6-32536438-C-T	AFR:0.74 AMR:0.38 EAS:0.56 EUR:0.57 SAS:0.88 10K:0.65	rs3957147-?		Other measurement	Seropositivity for hordeum vulgare (barley) peptide (twist_15602)	5.666	1E-8	GCST90293451	NR
6-32536438-C-T	AFR:0.74 AMR:0.38 EAS:0.56 EUR:0.57 SAS:0.88 10K:0.65	rs3957147-T	XXbac-BPG254F23.7	Body measurement	Hip circumference adjusted for BMI	0.0232882	5E-9	GCST012227	European
6-32439175-G-C	AFR:0.37 AMR:0.79 EAS:0.96 EUR:0.91 SAS:0.93 10K:0.81	rs535777-?	NR	Neurological disorder	Help-seeking from a GP	1.0362694	5E-6	GCST010011	European
6-32439175-G-C	AFR:0.37 AMR:0.79 EAS:0.96 EUR:0.91 SAS:0.93 10K:0.81	rs535777-G	NR	Neurological disorder	Help-seeking from a psychiatrist	1.0752687	1E-9	GCST010012	European
6-32439175-G-C	AFR:0.37 AMR:0.79 EAS:0.96 EUR:0.91 SAS:0.93 10K:0.81	rs535777-?		Other measurement	Depression	0.011	9E-10	GCST90239706	European, NR
6-32439175-G-C	AFR:0.37 AMR:0.79 EAS:0.96 EUR:0.91 SAS:0.93 10K:0.81	rs535777-G		Cancer	Cancer (pleiotropy)(bidirectional)		4E-12	GCST90011823	European
6-32533620-C-T	AFR:0.84 AMR:0.46 EAS:0.58 EUR:0.90 SAS:0.94 10K:0.70	rs9275576-T	HLA-DQA2	Other measurement	Coffee consumption (cups per day)	0.048	6E-9	GCST010108	European
6-32533620-C-T	AFR:0.84 AMR:0.46 EAS:0.58 EUR:0.90 SAS:0.94 10K:0.70	rs9275576-T		Other measurement	Secreted frizzled-related protein 3 levels	0.169	6E-18	GCST90249516	European

Epigenetic signals

Marker	Cell type	Range
H3K27me3	MG63	32476849-32481112

Fixation index Fst

The Fixation index Fst was adopted as the measure for assessing population differences.

NyuWa Global 10K T2T Variant Database

Variant Database and Imputation service with world population genome resource

Variant: 6-32478685-MEI-SVA

Reference: T2T-CHM13

T2T-specific: 6:32472837-32480832

Browser:

xQTL results for 6-32478685-MEI-SVA

LD results for 6-32478685-MEI-SVA

NyuWa Global 10K T2T Variant Database

Variant Database and Imputation service with world population genome resource

Variant: 6-32478685-MEI-SVA

Reference: T2T-CHM13 T2T-specific: 6:32472837-32480832

Browser: Browser

xQTL results for 6-32478685-MEI-SVA

LD results for 6-32478685-MEI-SVA

Reference: T2T-CHM13

T2T-specific: 6:32472837-32480832

Browser: