Variant report

Variant	rs7782140
Chromosome Location	chr7:38937978-38937979
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	chr7:38888643..38891197-chr7:38936286..38938382,2	MCF-7	breast:

Extended variants
information (count: 112 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10085487	0.82[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap]
rs1012976	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[EUR][1000 genomes];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];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10229055	1.00[CHB][hapmap]
rs10229531	0.89[YRI][hapmap]
rs10239904	0.81[EUR][1000 genomes]
rs10254354	0.82[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs10254873	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10264217	0.81[EUR][1000 genomes]
rs10266279	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10270427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10270483	0.81[EUR][1000 genomes]
rs10274968	0.89[YRI][hapmap]
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	0.91[EUR][1000 genomes]
rs12701656	1.00[ASN][1000 genomes]
rs12701657	1.00[ASN][1000 genomes]
rs12701661	1.00[CHB][hapmap];1.00[CHD][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	0.89[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]
rs2058073	0.84[AMR][1000 genomes]
rs2079546	0.83[AMR][1000 genomes];0.92[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];0.92[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[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2245773	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs2286089	0.82[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][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]
rs2392604	0.89[YRI][hapmap]
rs2392608	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2392610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[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	0.89[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];0.81[GIH][hapmap]
rs37477	1.00[JPT][hapmap]
rs37478	1.00[JPT][hapmap]
rs37479	1.00[JPT][hapmap]
rs4720300	0.82[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][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];0.93[EUR][1000 genomes]
rs4723804	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57969771	0.83[AFR][1000 genomes]
rs58060833	0.83[AFR][1000 genomes]
rs6462866	1.00[JPT][hapmap]
rs6462871	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs6462873	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[TSI][hapmap]
rs6462874	0.92[EUR][1000 genomes]
rs6947695	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[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]
rs6960945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6963090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6964985	0.83[AMR][1000 genomes];0.92[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];0.81[EUR][1000 genomes]
rs6974764	0.83[AMR][1000 genomes];0.92[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];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6976579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6976580	1.00[CHB][hapmap];0.89[EUR][1000 genomes]
rs6979423	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73370730	1.00[ASN][1000 genomes]
rs757685	1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs758087	1.00[JPT][hapmap]
rs758088	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7782277	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7783723	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7784065	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7784609	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7787423	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7789864	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7790054	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs7793250	1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7799887	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs7802052	1.00[ASN][1000 genomes]
rs7803488	0.82[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs9638945	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs976350	1.00[JPT][hapmap]
rs976352	1.00[ASN][1000 genomes]
rs9886108	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.92[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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7782140	VPS41	Cis_1M	lymphoblastoid	RTeQTL
rs7782140	VPS41	cis	multi-tissue	Pritchard

Chromatin state (count:105 , 50 per page) page: 1 2 3

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	chr7:38903800-38939600	Weak transcription	A549	lung
5	chr7:38903800-38947000	Weak transcription	Small Intestine	intestine
6	chr7:38906000-38947800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr7:38908000-38941000	Weak transcription	Colon Smooth Muscle	Colon
8	chr7:38908200-38938600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr7:38908800-38943000	Weak transcription	Esophagus	oesophagus
10	chr7:38908800-38947800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr7:38908800-38948000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr7:38909000-38947800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr7:38911800-38948200	Weak transcription	Aorta	Aorta
14	chr7:38916600-38941600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr7:38916800-38948200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr7:38918800-38948000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr7:38919400-38942200	Weak transcription	Pancreas	Pancrea
18	chr7:38920400-38940800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr7:38920800-38942400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr7:38921000-38938000	Weak transcription	Brain Anterior Caudate	brain
21	chr7:38921000-38946800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr7:38921800-38947800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr7:38925200-38947800	Weak transcription	HUVEC	blood vessel
24	chr7:38926400-38948000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr7:38926600-38941800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr7:38928000-38947400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr7:38928800-38942200	Weak transcription	NHDF-Ad	bronchial
28	chr7:38929200-38947800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr7:38930000-38947600	Weak transcription	NHLF	lung
30	chr7:38930200-38946800	Weak transcription	K562	blood
31	chr7:38930200-38947400	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr7:38930200-38947400	Weak transcription	HSMM	muscle
33	chr7:38930200-38947600	Weak transcription	Fetal Kidney	kidney
34	chr7:38930200-38947800	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr7:38931000-38945000	Weak transcription	Primary B cells from cord blood	blood
36	chr7:38931200-38947400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr7:38932200-38948000	Weak transcription	Psoas Muscle	Psoas
38	chr7:38932600-38938000	Strong transcription	Fetal Intestine Small	intestine
39	chr7:38932600-38938000	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr7:38932800-38948000	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr7:38933000-38941800	Weak transcription	Lung	lung
42	chr7:38933000-38942200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr7:38933000-38947800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr7:38933000-38948200	Weak transcription	Spleen	Spleen
45	chr7:38933200-38942200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr7:38933800-38938000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr7:38934000-38947800	Weak transcription	Brain Angular Gyrus	brain
48	chr7:38934200-38947600	Weak transcription	Fetal Brain Male	brain
49	chr7:38935800-38938000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr7:38935800-38938000	Weak transcription	Primary hematopoietic stem cells	blood

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