Variant report

Variant	rs7793250
Chromosome Location	chr7:38940400-38940401
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:38938879..38942255-chr7:38943779..38948503,4	MCF-7	breast:

Extended variants
information (count: 97 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10085487	1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1012976	1.00[CHB][hapmap]
rs10224856	1.00[CHB][hapmap]
rs10225415	1.00[CHB][hapmap]
rs10225550	1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10229055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10232614	1.00[ASN][1000 genomes]
rs10239757	1.00[ASN][1000 genomes]
rs10239904	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10242407	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10254354	1.00[CHB][hapmap]
rs10254873	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10264217	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10266279	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10270427	1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs10270483	0.88[EUR][1000 genomes]
rs10275873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10951574	1.00[CHB][hapmap]
rs11983387	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12701661	1.00[CHB][hapmap]
rs12701671	1.00[CHB][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13224619	1.00[CHB][hapmap]
rs13230196	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13231372	1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13235997	1.00[CHB][hapmap]
rs13236092	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13238093	1.00[ASN][1000 genomes]
rs1558111	1.00[CHB][hapmap]
rs17240051	0.81[EUR][1000 genomes]
rs2040878	1.00[CHB][hapmap]
rs2079546	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2108508	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2189854	1.00[CHB][hapmap]
rs2190667	1.00[CHB][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2190668	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2190670	1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2214667	1.00[CHB][hapmap]
rs2214668	1.00[CHB][hapmap]
rs2215032	1.00[CHB][hapmap]
rs2245773	1.00[CHB][hapmap]
rs2286089	1.00[CHB][hapmap]
rs2286093	1.00[CHB][hapmap]
rs2286101	1.00[CHB][hapmap]
rs2392599	1.00[CHB][hapmap]
rs2392608	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2392610	1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs34349310	1.00[ASN][1000 genomes]
rs34358406	1.00[ASN][1000 genomes]
rs35220172	0.81[EUR][1000 genomes]
rs35667896	1.00[ASN][1000 genomes]
rs36004953	1.00[ASN][1000 genomes]
rs36114334	1.00[ASN][1000 genomes]
rs36121032	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs37476	1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40445	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4275134	0.86[EUR][1000 genomes]
rs4720300	1.00[CHB][hapmap]
rs4723780	1.00[CHB][hapmap]
rs4723781	1.00[CHB][hapmap]
rs4723784	1.00[CHB][hapmap]
rs4723787	1.00[CHB][hapmap]
rs4723802	1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs4723804	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6462871	1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6462873	1.00[CHB][hapmap]
rs6462874	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6947695	1.00[CHB][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6949958	1.00[CHB][hapmap]
rs6951429	1.00[CHB][hapmap]
rs6960945	1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs6963090	1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6964985	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6967384	1.00[CHB][hapmap]
rs6971632	1.00[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6974764	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6975410	1.00[CHB][hapmap]
rs6976302	1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs6976579	1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs6976580	1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6978805	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6979423	1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs71548633	1.00[ASN][1000 genomes]
rs758088	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7782140	1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7782277	1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7783723	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784065	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784609	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7787423	1.00[CHB][hapmap]
rs7788663	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7789864	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7790054	1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7799887	1.00[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7803488	1.00[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9638945	1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9886108	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7793250	VPS41	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38886200-38947800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr7:38889400-38948200	Weak transcription	Gastric	stomach
3	chr7:38903800-38947000	Weak transcription	Small Intestine	intestine
4	chr7:38906000-38947800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr7:38908000-38941000	Weak transcription	Colon Smooth Muscle	Colon
6	chr7:38908800-38943000	Weak transcription	Esophagus	oesophagus
7	chr7:38908800-38947800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr7:38908800-38948000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr7:38909000-38947800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr7:38911800-38948200	Weak transcription	Aorta	Aorta
11	chr7:38916600-38941600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr7:38916800-38948200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr7:38918800-38948000	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr7:38919400-38942200	Weak transcription	Pancreas	Pancrea
15	chr7:38920400-38940800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr7:38920800-38942400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr7:38921000-38946800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr7:38921800-38947800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr7:38925200-38947800	Weak transcription	HUVEC	blood vessel
20	chr7:38926400-38948000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr7:38926600-38941800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr7:38928000-38947400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr7:38928800-38942200	Weak transcription	NHDF-Ad	bronchial
24	chr7:38929200-38947800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr7:38930000-38947600	Weak transcription	NHLF	lung
26	chr7:38930200-38946800	Weak transcription	K562	blood
27	chr7:38930200-38947400	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr7:38930200-38947400	Weak transcription	HSMM	muscle
29	chr7:38930200-38947600	Weak transcription	Fetal Kidney	kidney
30	chr7:38930200-38947800	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr7:38931000-38945000	Weak transcription	Primary B cells from cord blood	blood
32	chr7:38931200-38947400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr7:38932200-38948000	Weak transcription	Psoas Muscle	Psoas
34	chr7:38932800-38948000	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr7:38933000-38941800	Weak transcription	Lung	lung
36	chr7:38933000-38942200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr7:38933000-38947800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr7:38933000-38948200	Weak transcription	Spleen	Spleen
39	chr7:38933200-38942200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr7:38934000-38947800	Weak transcription	Brain Angular Gyrus	brain
41	chr7:38934200-38947600	Weak transcription	Fetal Brain Male	brain
42	chr7:38935800-38942200	Weak transcription	Left Ventricle	heart
43	chr7:38935800-38946800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr7:38935800-38947800	Weak transcription	Fetal Stomach	stomach
45	chr7:38935800-38948000	Weak transcription	Placenta	Placenta
46	chr7:38935800-38948000	Weak transcription	Ovary	ovary
47	chr7:38936000-38947400	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr7:38936000-38947600	Weak transcription	Fetal Lung	lung
49	chr7:38936000-38947800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr7:38936000-38947800	Weak transcription	Rectal Mucosa Donor 31	rectum

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