Variant report

Variant	rs6462871
Chromosome Location	chr7:38889235-38889236
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	chr7:38888643..38891197-chr7:38936286..38938382,2	MCF-7	breast:
2	chr7:38887343..38889713-chr7:38889792..38892384,2	MCF-7	breast:

Extended variants
information (count: 106 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10085487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1012976	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10224856	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10225415	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10225550	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10229055	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10232614	1.00[ASN][1000 genomes]
rs10239757	1.00[ASN][1000 genomes]
rs10239904	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10242407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10254354	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10254873	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10264217	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10266279	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10270427	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10270483	0.87[EUR][1000 genomes]
rs10275873	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10951574	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs11983387	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12701653	1.00[CHB][hapmap]
rs12701656	1.00[AFR][1000 genomes]
rs12701657	1.00[AFR][1000 genomes]
rs12701661	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs12701671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13224619	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs13230196	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13231372	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13235997	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs13236092	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13238093	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1558111	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs17240051	0.80[EUR][1000 genomes]
rs17680342	0.82[CEU][hapmap]
rs2040878	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2058073	0.88[AMR][1000 genomes]
rs2079546	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2108508	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2189854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes]
rs2190667	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2190668	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2190670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2214667	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2214668	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2215032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2245773	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2286089	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2286093	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2286101	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2392599	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2392608	0.82[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2392610	0.82[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs34349310	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34358406	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34621392	1.00[AFR][1000 genomes]
rs34886315	1.00[AFR][1000 genomes]
rs35220172	0.80[EUR][1000 genomes]
rs35667896	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs36004953	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs36114334	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs36121032	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs37476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40445	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4275134	0.85[EUR][1000 genomes]
rs4720300	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs4723780	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs4723781	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs4723784	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs4723787	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs4723802	0.82[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs4723804	0.91[EUR][1000 genomes]
rs6462873	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs6462874	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6947695	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6949958	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs6951429	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs6960945	0.82[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs6963090	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs6964985	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6967384	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs6971632	0.82[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6974764	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6975410	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs6976302	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs6976579	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs6976580	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6978805	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6979423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71548633	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs758088	0.91[EUR][1000 genomes]
rs7782140	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs7782277	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs7783723	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784065	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784609	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7787423	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7788663	0.86[EUR][1000 genomes]
rs7789864	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7790054	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7793250	1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7799887	0.82[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7803488	1.00[CHB][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9638945	0.82[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs976352	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs9886108	0.82[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	nsv1032637	chr7:38832627-38902723	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6462871	VPS41	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38835600-38900800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:38858600-38901600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr7:38858800-38907600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr7:38859000-38895200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr7:38859800-38900800	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr7:38860600-38900200	Weak transcription	Fetal Intestine Large	intestine
7	chr7:38867400-38905200	Weak transcription	Left Ventricle	heart
8	chr7:38870000-38895600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr7:38870200-38895600	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr7:38871400-38905800	Weak transcription	Aorta	Aorta
11	chr7:38871400-38920000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr7:38871600-38906000	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr7:38873000-38907600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr7:38873200-38919200	Weak transcription	Pancreas	Pancrea
15	chr7:38875800-38897400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr7:38876400-38906200	Weak transcription	Duodenum Mucosa	Duodenum
17	chr7:38877000-38895600	Weak transcription	Spleen	Spleen
18	chr7:38877200-38900800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr7:38877200-38901200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr7:38877400-38896200	Weak transcription	Primary hematopoietic stem cells	blood
21	chr7:38879800-38891800	Weak transcription	Right Atrium	heart
22	chr7:38879800-38938000	Weak transcription	Right Ventricle	heart
23	chr7:38880200-38897600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr7:38880600-38900600	Weak transcription	Adipose Nuclei	Adipose
25	chr7:38880800-38905600	Weak transcription	Fetal Muscle Leg	muscle
26	chr7:38881200-38895000	Weak transcription	GM12878-XiMat	blood
27	chr7:38881200-38898000	Weak transcription	HSMMtube	muscle
28	chr7:38881200-38898000	Weak transcription	NHLF	lung
29	chr7:38881200-38900000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr7:38881200-38907600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr7:38881200-38919200	Weak transcription	Psoas Muscle	Psoas
32	chr7:38881400-38898000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr7:38882000-38890200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr7:38883400-38907600	Weak transcription	Esophagus	oesophagus
35	chr7:38884600-38905600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr7:38885000-38893800	Weak transcription	Small Intestine	intestine
37	chr7:38885000-38900800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr7:38885800-38897200	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr7:38886200-38890600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr7:38886200-38893000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr7:38886200-38901400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr7:38886200-38947800	Weak transcription	Stomach Smooth Muscle	stomach
43	chr7:38886400-38898000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr7:38886400-38907400	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr7:38886400-38907400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr7:38886400-38907600	Weak transcription	Rectal Smooth Muscle	rectum
47	chr7:38886600-38890600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr7:38886600-38901200	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr7:38886600-38907200	Weak transcription	Colon Smooth Muscle	Colon
50	chr7:38886800-38889400	Weak transcription	NHDF-Ad	bronchial

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