Variant report

Variant	rs2190668
Chromosome Location	chr7:38865122-38865123
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10085487	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1012976	0.88[EUR][1000 genomes]
rs10224856	0.81[EUR][1000 genomes]
rs10225415	0.81[EUR][1000 genomes]
rs10225550	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10229055	1.00[ASN][1000 genomes]
rs10232614	1.00[ASN][1000 genomes]
rs10239757	1.00[ASN][1000 genomes]
rs10239904	1.00[ASN][1000 genomes]
rs10242407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10254354	0.81[EUR][1000 genomes]
rs10254873	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10264217	1.00[ASN][1000 genomes]
rs10266279	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10270427	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs10275873	1.00[ASN][1000 genomes]
rs10951574	0.81[EUR][1000 genomes]
rs11983387	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12701656	1.00[AFR][1000 genomes]
rs12701657	1.00[AFR][1000 genomes]
rs12701671	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13230196	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13231372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13236092	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13238093	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2040878	0.81[EUR][1000 genomes]
rs2058073	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2079546	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2108508	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2189854	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2190667	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2190670	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2214667	0.81[EUR][1000 genomes]
rs2214668	0.81[EUR][1000 genomes]
rs2215032	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2245773	0.81[EUR][1000 genomes]
rs2286089	0.81[EUR][1000 genomes]
rs2286093	0.81[EUR][1000 genomes]
rs2286101	0.81[EUR][1000 genomes]
rs2392599	0.81[EUR][1000 genomes]
rs2392608	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34349310	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34358406	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34621392	1.00[AFR][1000 genomes]
rs34886315	1.00[AFR][1000 genomes]
rs35667896	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36004953	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36114334	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36121032	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs37476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40445	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4720300	0.81[EUR][1000 genomes]
rs4723780	0.81[EUR][1000 genomes]
rs4723781	0.81[EUR][1000 genomes]
rs4723784	0.81[EUR][1000 genomes]
rs4723787	0.81[EUR][1000 genomes]
rs6462871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6462874	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6947695	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6949958	0.81[EUR][1000 genomes]
rs6951429	0.81[EUR][1000 genomes]
rs6964985	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6967384	0.81[EUR][1000 genomes]
rs6971632	1.00[ASN][1000 genomes]
rs6974764	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6975410	0.81[EUR][1000 genomes]
rs6976580	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6978805	1.00[ASN][1000 genomes]
rs6979423	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs71548633	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7783723	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784065	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784609	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7787423	0.81[EUR][1000 genomes]
rs7789864	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7790054	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7793250	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7799887	1.00[ASN][1000 genomes]
rs7802052	0.81[EUR][1000 genomes]
rs7803488	1.00[ASN][1000 genomes]
rs9638945	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs976352	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9886108	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032637	chr7:38832627-38902723	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv887966	chr7:38835035-38933942	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2190668	VPS41	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38831000-38871200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr7:38831800-38867800	Weak transcription	Fetal Thymus	thymus
3	chr7:38835200-38865200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr7:38835600-38900800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr7:38839800-38871000	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr7:38842000-38865400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr7:38847400-38869800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr7:38847800-38866800	Weak transcription	Brain Substantia Nigra	brain
9	chr7:38850200-38865400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr7:38850600-38869600	Weak transcription	Stomach Mucosa	stomach
11	chr7:38851600-38867000	Weak transcription	Gastric	stomach
12	chr7:38854000-38870400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr7:38855400-38865400	Weak transcription	Osteobl	bone
14	chr7:38855600-38871000	Weak transcription	HepG2	liver
15	chr7:38856000-38865200	Weak transcription	NHDF-Ad	bronchial
16	chr7:38856000-38871000	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr7:38856200-38865400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr7:38856200-38871200	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr7:38856800-38865400	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr7:38857200-38867200	Weak transcription	Esophagus	oesophagus
21	chr7:38857600-38865200	Weak transcription	Placenta	Placenta
22	chr7:38857600-38865800	Weak transcription	HSMMtube	muscle
23	chr7:38857600-38871800	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr7:38857800-38865200	Weak transcription	Colon Smooth Muscle	Colon
25	chr7:38858000-38865600	Weak transcription	Liver	Liver
26	chr7:38858000-38870600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr7:38858200-38865200	Weak transcription	Ovary	ovary
28	chr7:38858200-38867000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr7:38858200-38868600	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr7:38858400-38865400	Weak transcription	Left Ventricle	heart
31	chr7:38858400-38871800	Weak transcription	Lung	lung
32	chr7:38858600-38901600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr7:38858800-38865200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr7:38858800-38907600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr7:38859000-38865200	Weak transcription	Psoas Muscle	Psoas
36	chr7:38859000-38865400	Weak transcription	Stomach Smooth Muscle	stomach
37	chr7:38859000-38872800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr7:38859000-38895200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr7:38859200-38865400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr7:38859400-38865600	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr7:38859400-38868000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr7:38859400-38869400	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr7:38859800-38865400	Weak transcription	Pancreas	Pancrea
44	chr7:38859800-38900800	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr7:38860000-38870800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr7:38860600-38900200	Weak transcription	Fetal Intestine Large	intestine
47	chr7:38860800-38865600	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr7:38863000-38865200	Weak transcription	Aorta	Aorta
49	chr7:38863000-38865400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr7:38863000-38865400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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