Variant report

Variant	rs6947695
Chromosome Location	chr7:38920556-38920557
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:38915745..38917788-chr7:38919334..38921629,2	K562	blood:

Extended variants
information (count: 105 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10085487	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1012976	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs10224856	1.00[CHB][hapmap]
rs10225415	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs10225550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10229055	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10232614	1.00[ASN][1000 genomes]
rs10239757	1.00[ASN][1000 genomes]
rs10239904	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10242407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10254354	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs10254873	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10264217	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10266279	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10270427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10270483	0.88[EUR][1000 genomes]
rs10275873	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10951574	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs11983387	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12701653	1.00[CHB][hapmap]
rs12701656	1.00[AFR][1000 genomes]
rs12701657	1.00[AFR][1000 genomes]
rs12701661	1.00[CHB][hapmap]
rs12701671	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13224619	1.00[CHB][hapmap]
rs13230196	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13231372	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13235997	1.00[CHB][hapmap]
rs13236092	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13238093	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1558111	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs17240051	0.81[EUR][1000 genomes]
rs2040878	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs2058073	0.88[AMR][1000 genomes]
rs2079546	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2108508	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2189854	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes]
rs2190667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2190668	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2190670	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2214667	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs2214668	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs2215032	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2245773	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs2286089	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs2286093	1.00[CHB][hapmap]
rs2286101	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs2392599	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs2392608	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2392610	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][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]
rs35220172	0.81[EUR][1000 genomes]
rs35667896	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs36004953	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs36114334	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs36121032	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs37476	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40445	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4275134	0.86[EUR][1000 genomes]
rs4720300	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs4723780	1.00[CHB][hapmap]
rs4723781	1.00[CHB][hapmap]
rs4723784	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs4723787	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs4723802	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs4723804	0.92[EUR][1000 genomes]
rs6462871	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6462873	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs6462874	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6949958	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs6951429	1.00[CHB][hapmap]
rs6960945	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs6963090	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs6964985	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6967384	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs6971632	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6974764	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6975410	1.00[CHB][hapmap]
rs6976302	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs6976579	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs6976580	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6978805	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6979423	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71548633	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs758088	0.92[EUR][1000 genomes]
rs7782140	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs7782277	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs7783723	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784065	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784609	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7787423	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs7788663	0.87[EUR][1000 genomes]
rs7789864	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7790054	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7793250	1.00[CHB][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7799887	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7803488	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9638945	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs976352	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs9886108	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];1.00[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	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
2	nsv830967	chr7:38913837-39069253	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6947695	VPS41	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38879800-38938000	Weak transcription	Right Ventricle	heart
2	chr7:38886200-38947800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr7:38889400-38948200	Weak transcription	Gastric	stomach
4	chr7:38889600-38932600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr7:38893800-38925600	Weak transcription	Thymus	Thymus
6	chr7:38898600-38928800	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr7:38899200-38924200	Weak transcription	Fetal Kidney	kidney
8	chr7:38903800-38939600	Weak transcription	A549	lung
9	chr7:38903800-38947000	Weak transcription	Small Intestine	intestine
10	chr7:38905000-38925600	Weak transcription	Fetal Intestine Small	intestine
11	chr7:38905600-38937800	Weak transcription	Colonic Mucosa	Colon
12	chr7:38906000-38947800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr7:38907800-38922400	Weak transcription	HepG2	liver
14	chr7:38908000-38941000	Weak transcription	Colon Smooth Muscle	Colon
15	chr7:38908200-38924200	Weak transcription	Lung	lung
16	chr7:38908200-38925600	Weak transcription	Fetal Stomach	stomach
17	chr7:38908200-38932800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr7:38908200-38933800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr7:38908200-38935000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr7:38908200-38935400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr7:38908200-38935400	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr7:38908200-38938600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr7:38908600-38925800	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr7:38908600-38935200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr7:38908800-38925000	Weak transcription	Fetal Muscle Leg	muscle
26	chr7:38908800-38925600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr7:38908800-38925800	Weak transcription	Fetal Muscle Trunk	muscle
28	chr7:38908800-38932600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr7:38908800-38934200	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr7:38908800-38935400	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr7:38908800-38943000	Weak transcription	Esophagus	oesophagus
32	chr7:38908800-38947800	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr7:38908800-38948000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr7:38909000-38920600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr7:38909000-38933800	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr7:38909000-38934200	Weak transcription	Duodenum Mucosa	Duodenum
37	chr7:38909000-38947800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr7:38910200-38929600	Weak transcription	Primary T cells from cord blood	blood
39	chr7:38911800-38948200	Weak transcription	Aorta	Aorta
40	chr7:38912000-38932800	Weak transcription	Spleen	Spleen
41	chr7:38913600-38921000	Weak transcription	NHEK	skin
42	chr7:38913600-38921600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr7:38913800-38925800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr7:38914000-38934200	Weak transcription	Liver	Liver
45	chr7:38914200-38935000	Weak transcription	Dnd41	blood
46	chr7:38916600-38941600	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr7:38916800-38921600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr7:38916800-38923000	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr7:38916800-38948200	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr7:38917600-38934000	Weak transcription	Ovary	ovary

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