Variant report

Variant	rs6462874
Chromosome Location	chr7:38934030-38934031
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:38933211..38936030-chr7:38947333..38948872,2	MCF-7	breast:
2	chr7:38932121..38934531-chr7:38942831..38944906,2	K562	blood:
3	chr7:38929214..38932230-chr7:38932411..38935645,3	K562	blood:

Variant related genes	Relation type
ENSG00000006715	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10085487	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10225550	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10229055	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	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10254873	0.83[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	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10270427	0.92[EUR][1000 genomes]
rs10270483	0.88[EUR][1000 genomes]
rs10275873	1.00[ASN][1000 genomes]
rs11983387	0.99[EUR][1000 genomes]
rs12701671	1.00[ASN][1000 genomes]
rs13230196	1.00[ASN][1000 genomes]
rs13231372	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13236092	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13238093	1.00[ASN][1000 genomes]
rs17240051	0.81[EUR][1000 genomes]
rs2079546	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2108508	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2190667	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2190668	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2190670	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2392608	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2392610	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	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs37476	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40445	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4275134	0.86[EUR][1000 genomes]
rs4723802	0.88[EUR][1000 genomes]
rs4723804	0.92[EUR][1000 genomes]
rs6462871	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6947695	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6960945	0.82[EUR][1000 genomes]
rs6963090	0.92[EUR][1000 genomes]
rs6964985	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6971632	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6974764	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6976302	0.92[EUR][1000 genomes]
rs6976579	0.92[EUR][1000 genomes]
rs6976580	0.97[EUR][1000 genomes]
rs6978805	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6979423	0.91[EUR][1000 genomes]
rs71548633	1.00[ASN][1000 genomes]
rs758088	0.92[EUR][1000 genomes]
rs7782140	0.92[EUR][1000 genomes]
rs7782277	0.92[EUR][1000 genomes]
rs7783723	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784065	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784609	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7788663	0.87[EUR][1000 genomes]
rs7789864	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7790054	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7793250	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7799887	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7803488	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9638945	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9886108	0.83[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
rs6462874	VPS41	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 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	chr7:38905600-38937800	Weak transcription	Colonic Mucosa	Colon
7	chr7:38906000-38947800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr7:38908000-38941000	Weak transcription	Colon Smooth Muscle	Colon
9	chr7:38908200-38935000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr7:38908200-38935400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr7:38908200-38935400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr7:38908200-38938600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr7:38908600-38935200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr7:38908800-38934200	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr7:38908800-38935400	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr7:38908800-38943000	Weak transcription	Esophagus	oesophagus
17	chr7:38908800-38947800	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr7:38908800-38948000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr7:38909000-38934200	Weak transcription	Duodenum Mucosa	Duodenum
20	chr7:38909000-38947800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr7:38911800-38948200	Weak transcription	Aorta	Aorta
22	chr7:38914000-38934200	Weak transcription	Liver	Liver
23	chr7:38914200-38935000	Weak transcription	Dnd41	blood
24	chr7:38916600-38941600	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr7:38916800-38948200	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr7:38918800-38934200	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr7:38918800-38948000	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr7:38919400-38942200	Weak transcription	Pancreas	Pancrea
29	chr7:38920200-38934200	Weak transcription	Primary B cells from peripheral blood	blood
30	chr7:38920400-38940800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr7:38920600-38935000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr7:38920600-38935000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr7:38920600-38935400	Weak transcription	Brain Hippocampus Middle	brain
34	chr7:38920600-38936200	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr7:38920800-38934600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr7:38920800-38942400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr7:38921000-38938000	Weak transcription	Brain Anterior Caudate	brain
38	chr7:38921000-38946800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr7:38921200-38935600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr7:38921800-38947800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr7:38925200-38947800	Weak transcription	HUVEC	blood vessel
42	chr7:38925800-38935000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr7:38925800-38935400	Weak transcription	Thymus	Thymus
44	chr7:38926200-38934400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr7:38926200-38935000	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr7:38926400-38948000	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr7:38926600-38941800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr7:38926800-38934600	Weak transcription	Fetal Stomach	stomach
49	chr7:38927400-38935600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr7:38928000-38947400	Weak transcription	Brain Cingulate Gyrus	brain

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