Variant report

Variant	rs10270483
Chromosome Location	chr7:38928918-38928919
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10225550	0.88[EUR][1000 genomes]
rs10239904	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10254873	0.88[EUR][1000 genomes]
rs10264217	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10266279	0.87[EUR][1000 genomes]
rs10269756	0.84[AFR][1000 genomes]
rs10270427	0.81[EUR][1000 genomes]
rs11980197	0.84[AFR][1000 genomes]
rs11983387	0.87[EUR][1000 genomes]
rs17240051	0.90[EUR][1000 genomes]
rs2079546	0.88[EUR][1000 genomes]
rs2190667	0.88[EUR][1000 genomes]
rs2392606	0.84[AFR][1000 genomes]
rs2392608	0.88[EUR][1000 genomes]
rs2392610	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28369620	0.84[AFR][1000 genomes]
rs28460817	0.81[AFR][1000 genomes]
rs35220172	0.90[EUR][1000 genomes]
rs4275134	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4723804	0.81[EUR][1000 genomes]
rs59978834	0.83[AFR][1000 genomes]
rs6462871	0.87[EUR][1000 genomes]
rs6462873	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6462874	0.88[EUR][1000 genomes]
rs6947695	0.88[EUR][1000 genomes]
rs6948026	0.84[AFR][1000 genomes]
rs6960945	0.93[EUR][1000 genomes]
rs6963090	0.81[EUR][1000 genomes]
rs6964985	0.88[EUR][1000 genomes]
rs6971632	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6973415	0.84[AFR][1000 genomes]
rs6974764	0.88[EUR][1000 genomes]
rs6974795	0.84[AFR][1000 genomes]
rs6976302	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6976579	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6976580	0.86[EUR][1000 genomes]
rs6978805	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73368521	0.81[AFR][1000 genomes]
rs758088	0.81[EUR][1000 genomes]
rs7776996	0.84[AFR][1000 genomes]
rs7782140	0.81[EUR][1000 genomes]
rs7782277	0.81[EUR][1000 genomes]
rs7783723	0.88[EUR][1000 genomes]
rs7784065	0.88[EUR][1000 genomes]
rs7784609	0.88[EUR][1000 genomes]
rs7789864	0.88[EUR][1000 genomes]
rs7793250	0.88[EUR][1000 genomes]
rs7799887	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7803488	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9638945	0.88[EUR][1000 genomes]
rs9886108	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
rs10270483	VPS41	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:80 , 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	chr7:38910200-38929600	Weak transcription	Primary T cells from cord blood	blood
27	chr7:38911800-38948200	Weak transcription	Aorta	Aorta
28	chr7:38912000-38932800	Weak transcription	Spleen	Spleen
29	chr7:38914000-38934200	Weak transcription	Liver	Liver
30	chr7:38914200-38935000	Weak transcription	Dnd41	blood
31	chr7:38916600-38941600	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr7:38916800-38948200	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr7:38917600-38934000	Weak transcription	Ovary	ovary
34	chr7:38918800-38929800	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr7:38918800-38934200	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr7:38918800-38948000	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr7:38919000-38929800	Weak transcription	Primary B cells from cord blood	blood
38	chr7:38919000-38932800	Weak transcription	Left Ventricle	heart
39	chr7:38919400-38942200	Weak transcription	Pancreas	Pancrea
40	chr7:38920200-38929200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr7:38920200-38934200	Weak transcription	Primary B cells from peripheral blood	blood
42	chr7:38920400-38940800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr7:38920600-38935000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr7:38920600-38935000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr7:38920600-38935400	Weak transcription	Brain Hippocampus Middle	brain
46	chr7:38920600-38936200	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr7:38920800-38934600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr7:38920800-38942400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr7:38921000-38930000	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr7:38921000-38938000	Weak transcription	Brain Anterior Caudate	brain

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