Variant report

Variant	rs4723802
Chromosome Location	chr7:38913934-38913935
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:38906917..38908871-chr7:38912756..38915741,2	MCF-7	breast:
2	chr7:38900320..38904154-chr7:38910727..38914259,3	K562	blood:
3	chr7:38913005..38915768-chr7:38916494..38919026,3	K562	blood:

Extended variants
information (count: 94 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:92)

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]
rs10224856	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10225415	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10225550	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs10229055	1.00[CHB][hapmap]
rs10254354	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10254873	0.88[EUR][1000 genomes]
rs10266279	0.87[EUR][1000 genomes]
rs10270427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10275873	1.00[CHB][hapmap]
rs10951574	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10951575	1.00[JPT][hapmap]
rs11983387	0.87[EUR][1000 genomes]
rs12701653	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12701661	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12701671	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs13224619	1.00[CHB][hapmap];1.00[JPT][hapmap]
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]
rs1558111	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs17240051	0.83[EUR][1000 genomes]
rs2040878	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2058073	0.89[AMR][1000 genomes]
rs2079546	0.88[EUR][1000 genomes]
rs2107742	1.00[JPT][hapmap]
rs2189854	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2190667	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[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]
rs2214668	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2215032	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2245773	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2286089	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2286093	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2286101	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2286103	1.00[JPT][hapmap]
rs2392599	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2392608	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs2392610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs35220172	0.83[EUR][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]
rs4720300	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs4720302	1.00[JPT][hapmap]
rs4723780	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4723781	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4723784	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4723786	1.00[JPT][hapmap]
rs4723787	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4723804	0.93[EUR][1000 genomes]
rs6462866	1.00[JPT][hapmap]
rs6462871	0.82[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs6462873	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs6462874	0.88[EUR][1000 genomes]
rs6947695	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs6949958	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6951429	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6960945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs6963090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs6964985	0.88[EUR][1000 genomes]
rs6967384	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6971632	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs6974764	0.88[EUR][1000 genomes]
rs6975410	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6976302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs6976579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs6976580	1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs6979423	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs757685	1.00[JPT][hapmap]
rs758087	1.00[JPT][hapmap]
rs758088	0.93[EUR][1000 genomes]
rs7782140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs7782277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs7783723	0.88[EUR][1000 genomes]
rs7784065	0.88[EUR][1000 genomes]
rs7784609	0.88[EUR][1000 genomes]
rs7787423	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7789864	0.88[EUR][1000 genomes]
rs7790054	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs7793250	1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs7799887	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7803488	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs9638945	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs976350	1.00[JPT][hapmap]
rs976352	0.84[AMR][1000 genomes]
rs9886108	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][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
rs4723802	VPS41	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38871400-38920000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr7:38873200-38919200	Weak transcription	Pancreas	Pancrea
3	chr7:38879800-38938000	Weak transcription	Right Ventricle	heart
4	chr7:38881200-38919200	Weak transcription	Psoas Muscle	Psoas
5	chr7:38886200-38947800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr7:38889400-38948200	Weak transcription	Gastric	stomach
7	chr7:38889600-38932600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr7:38893800-38925600	Weak transcription	Thymus	Thymus
9	chr7:38898400-38920000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr7:38898600-38914200	Weak transcription	NHLF	lung
11	chr7:38898600-38928800	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr7:38899200-38924200	Weak transcription	Fetal Kidney	kidney
13	chr7:38901800-38920000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr7:38903600-38917400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr7:38903800-38939600	Weak transcription	A549	lung
16	chr7:38903800-38947000	Weak transcription	Small Intestine	intestine
17	chr7:38905000-38925600	Weak transcription	Fetal Intestine Small	intestine
18	chr7:38905600-38937800	Weak transcription	Colonic Mucosa	Colon
19	chr7:38906000-38920000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr7:38906000-38947800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr7:38907800-38919800	Weak transcription	Brain Hippocampus Middle	brain
22	chr7:38907800-38922400	Weak transcription	HepG2	liver
23	chr7:38908000-38920000	Weak transcription	Fetal Brain Male	brain
24	chr7:38908000-38941000	Weak transcription	Colon Smooth Muscle	Colon
25	chr7:38908200-38916600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr7:38908200-38917600	Weak transcription	Primary hematopoietic stem cells	blood
27	chr7:38908200-38917600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr7:38908200-38918400	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr7:38908200-38918400	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr7:38908200-38918600	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr7:38908200-38919600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr7:38908200-38919600	Weak transcription	Brain Anterior Caudate	brain
33	chr7:38908200-38920200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr7:38908200-38920200	Weak transcription	Brain Angular Gyrus	brain
35	chr7:38908200-38924200	Weak transcription	Lung	lung
36	chr7:38908200-38925600	Weak transcription	Fetal Stomach	stomach
37	chr7:38908200-38932800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr7:38908200-38933800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr7:38908200-38935000	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr7:38908200-38935400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr7:38908200-38935400	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr7:38908200-38938600	Weak transcription	Rectal Smooth Muscle	rectum
43	chr7:38908400-38918200	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr7:38908600-38916400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr7:38908600-38919200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr7:38908600-38925800	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr7:38908600-38935200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr7:38908800-38915400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr7:38908800-38916200	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr7:38908800-38916600	Weak transcription	Ovary	ovary

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