Variant report

Variant	rs6960945
Chromosome Location	chr7:38907356-38907357
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:38906776..38909465-chr7:38940924..38943623,2	K562	blood:
2	chr7:38906917..38908871-chr7:38912756..38915741,2	MCF-7	breast:

Extended variants
information (count: 110 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10085487	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs1012976	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10224856	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10225415	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10225550	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs10229055	1.00[CHB][hapmap]
rs10239904	0.93[EUR][1000 genomes]
rs10254354	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10254873	0.82[EUR][1000 genomes]
rs10264217	0.93[EUR][1000 genomes]
rs10266279	0.80[EUR][1000 genomes]
rs10270427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10270483	0.93[EUR][1000 genomes]
rs10275873	1.00[CHB][hapmap]
rs10951574	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10951575	1.00[JPT][hapmap]
rs11983387	0.80[EUR][1000 genomes]
rs12701653	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12701656	1.00[ASN][1000 genomes]
rs12701657	1.00[ASN][1000 genomes]
rs12701661	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12701671	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs13224619	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13224857	1.00[ASN][1000 genomes]
rs13229445	1.00[ASN][1000 genomes]
rs13230196	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13231372	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs13235997	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1558111	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs17240051	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2040878	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2079546	0.82[EUR][1000 genomes]
rs2107742	1.00[JPT][hapmap]
rs2189854	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2190667	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs2190670	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs2214667	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2214668	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2215032	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2245773	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2286089	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2286093	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2286101	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2286103	1.00[JPT][hapmap]
rs2392599	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2392608	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs2392610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34621392	1.00[ASN][1000 genomes]
rs34886315	1.00[ASN][1000 genomes]
rs34997080	1.00[ASN][1000 genomes]
rs35220172	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35400125	1.00[ASN][1000 genomes]
rs35816439	1.00[ASN][1000 genomes]
rs35843038	1.00[ASN][1000 genomes]
rs37472	1.00[JPT][hapmap]
rs37473	1.00[JPT][hapmap]
rs37476	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs37477	1.00[JPT][hapmap]
rs37478	1.00[JPT][hapmap]
rs37479	1.00[JPT][hapmap]
rs3801127	0.90[YRI][hapmap]
rs4275134	0.90[EUR][1000 genomes]
rs4720300	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4720302	1.00[JPT][hapmap]
rs4723780	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4723781	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4723784	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4723786	1.00[JPT][hapmap]
rs4723787	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4723802	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs4723804	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6462866	1.00[JPT][hapmap]
rs6462871	0.82[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs6462873	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs6462874	0.82[EUR][1000 genomes]
rs6947695	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs6949958	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6951429	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6963090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6964985	0.82[EUR][1000 genomes]
rs6967384	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6971632	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs6974764	0.82[EUR][1000 genomes]
rs6975410	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6976302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6976579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6976580	1.00[CHB][hapmap]
rs6978805	0.90[EUR][1000 genomes]
rs6979423	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73370730	1.00[ASN][1000 genomes]
rs757685	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs758087	1.00[JPT][hapmap]
rs758088	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7782140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7782277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7783723	0.82[EUR][1000 genomes]
rs7784065	0.82[EUR][1000 genomes]
rs7784609	0.82[EUR][1000 genomes]
rs7787423	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7789864	0.82[EUR][1000 genomes]
rs7790054	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs7793250	1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs7799887	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs7802052	1.00[ASN][1000 genomes]
rs7803488	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs9638945	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs976350	1.00[JPT][hapmap]
rs976352	1.00[ASN][1000 genomes]
rs9886108	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6960945	VPS41	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38858800-38907600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr7:38871400-38920000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr7:38873000-38907600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr7:38873200-38919200	Weak transcription	Pancreas	Pancrea
5	chr7:38879800-38938000	Weak transcription	Right Ventricle	heart
6	chr7:38881200-38907600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr7:38881200-38919200	Weak transcription	Psoas Muscle	Psoas
8	chr7:38883400-38907600	Weak transcription	Esophagus	oesophagus
9	chr7:38886200-38947800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr7:38886400-38907400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr7:38886400-38907400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr7:38886400-38907600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr7:38887200-38907400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr7:38889400-38907400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr7:38889400-38909600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr7:38889400-38948200	Weak transcription	Gastric	stomach
17	chr7:38889600-38932600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr7:38893800-38925600	Weak transcription	Thymus	Thymus
19	chr7:38896000-38907600	Weak transcription	Spleen	Spleen
20	chr7:38897600-38907400	Weak transcription	Brain Angular Gyrus	brain
21	chr7:38897600-38909000	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr7:38898000-38907600	Weak transcription	HSMM	muscle
23	chr7:38898200-38909200	Weak transcription	NH-A	brain
24	chr7:38898400-38920000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr7:38898600-38907400	Weak transcription	HSMMtube	muscle
26	chr7:38898600-38907400	Weak transcription	Osteobl	bone
27	chr7:38898600-38907600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr7:38898600-38907600	Weak transcription	NHDF-Ad	bronchial
29	chr7:38898600-38914200	Weak transcription	NHLF	lung
30	chr7:38898600-38928800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr7:38898800-38912200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr7:38899200-38924200	Weak transcription	Fetal Kidney	kidney
33	chr7:38899400-38907600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr7:38901400-38907400	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr7:38901600-38907600	Weak transcription	Fetal Thymus	thymus
36	chr7:38901800-38907600	Weak transcription	Placenta	Placenta
37	chr7:38901800-38920000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr7:38902200-38910800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr7:38902600-38907400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr7:38902600-38910200	Weak transcription	Brain Germinal Matrix	brain
41	chr7:38903600-38917400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr7:38903800-38909800	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr7:38903800-38910000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr7:38903800-38913600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr7:38903800-38939600	Weak transcription	A549	lung
46	chr7:38903800-38947000	Weak transcription	Small Intestine	intestine
47	chr7:38904000-38910200	Weak transcription	HUVEC	blood vessel
48	chr7:38904400-38908800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr7:38904400-38908800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr7:38904400-38913200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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