Variant report

Variant	rs6462873
Chromosome Location	chr7:38930009-38930010
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	chr7:38929214..38932230-chr7:38932411..38935645,3	K562	blood:
2	chr7:38902352..38905123-chr7:38929723..38931780,2	MCF-7	breast:

Extended variants
information (count: 76 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10085487	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap]
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]
rs10229055	1.00[CHB][hapmap]
rs10239904	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10254354	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs10264217	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10270427	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10270483	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10275873	1.00[CHB][hapmap]
rs10951574	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs12701661	1.00[CHB][hapmap];0.82[MEX][hapmap]
rs12701671	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs13224619	1.00[CHB][hapmap]
rs13230196	1.00[CHB][hapmap]
rs13231372	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs13235997	1.00[CHB][hapmap]
rs1558111	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs17240051	0.81[EUR][1000 genomes]
rs2040878	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs2189854	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs2190667	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2190670	0.82[CEU][hapmap];1.00[CHB][hapmap]
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]
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]
rs2392607	0.81[AFR][1000 genomes]
rs2392608	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2392610	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35220172	0.81[EUR][1000 genomes]
rs37476	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap]
rs4275134	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[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]
rs59978834	0.85[AFR][1000 genomes]
rs6462871	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs6945239	0.82[AFR][1000 genomes]
rs6947695	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs6948026	0.92[YRI][hapmap]
rs6949958	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs6951429	1.00[CHB][hapmap]
rs6955677	0.84[LWK][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes]
rs6960945	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs6963090	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs6967384	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs6971632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6973415	0.91[YRI][hapmap]
rs6975410	1.00[CHB][hapmap]
rs6976302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs6976579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs6976580	1.00[CHB][hapmap]
rs6978805	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6979423	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs73368521	0.84[AFR][1000 genomes]
rs7782140	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[TSI][hapmap]
rs7782277	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7787423	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs7790054	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs7793250	1.00[CHB][hapmap]
rs7799887	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7803488	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9638945	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs9886108	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6462873	VPS41	cis	parietal	SCAN
rs6462873	RAB3IL1	trans	brain	seeQTL
rs6462873	VPS41	cis	multi-tissue	Pritchard

Chromatin state (count:91 , 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	chr7:38903800-38939600	Weak transcription	A549	lung
6	chr7:38903800-38947000	Weak transcription	Small Intestine	intestine
7	chr7:38905600-38937800	Weak transcription	Colonic Mucosa	Colon
8	chr7:38906000-38947800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr7:38908000-38941000	Weak transcription	Colon Smooth Muscle	Colon
10	chr7:38908200-38932800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr7:38908200-38933800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr7:38908200-38935000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr7:38908200-38935400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr7:38908200-38935400	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr7:38908200-38938600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr7:38908600-38935200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr7:38908800-38932600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr7:38908800-38934200	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr7:38908800-38935400	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr7:38908800-38943000	Weak transcription	Esophagus	oesophagus
21	chr7:38908800-38947800	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr7:38908800-38948000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr7:38909000-38933800	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr7:38909000-38934200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr7:38909000-38947800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr7:38911800-38948200	Weak transcription	Aorta	Aorta
27	chr7:38912000-38932800	Weak transcription	Spleen	Spleen
28	chr7:38914000-38934200	Weak transcription	Liver	Liver
29	chr7:38914200-38935000	Weak transcription	Dnd41	blood
30	chr7:38916600-38941600	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr7:38916800-38948200	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr7:38917600-38934000	Weak transcription	Ovary	ovary
33	chr7:38918800-38934200	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr7:38918800-38948000	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr7:38919000-38932800	Weak transcription	Left Ventricle	heart
36	chr7:38919400-38942200	Weak transcription	Pancreas	Pancrea
37	chr7:38920200-38934200	Weak transcription	Primary B cells from peripheral blood	blood
38	chr7:38920400-38940800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr7:38920600-38935000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr7:38920600-38935000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr7:38920600-38935400	Weak transcription	Brain Hippocampus Middle	brain
42	chr7:38920600-38936200	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr7:38920800-38934600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr7:38920800-38942400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr7:38921000-38938000	Weak transcription	Brain Anterior Caudate	brain
46	chr7:38921000-38946800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr7:38921200-38935600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr7:38921800-38947800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr7:38923600-38932400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr7:38925000-38931200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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