Variant report

Variant	rs3784062
Chromosome Location	chr14:72090505-72090506
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:72038823..72040937-chr14:72089563..72092048,2	MCF-7	breast:

Extended variants
information (count: 133 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs10133626	1.00[JPT][hapmap]
rs10135680	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10138557	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10139519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1029570	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10483836	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10873246	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11848785	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1204995	0.86[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs1204996	1.00[JPT][hapmap]
rs12127	0.81[EUR][1000 genomes]
rs12433040	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12879243	0.88[EUR][1000 genomes]
rs12880188	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs12880291	0.81[EUR][1000 genomes]
rs12880611	0.89[EUR][1000 genomes]
rs12881643	0.86[EUR][1000 genomes]
rs12881957	0.86[EUR][1000 genomes]
rs12885344	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12887261	0.81[EUR][1000 genomes]
rs12889866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs12892512	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12894016	0.88[EUR][1000 genomes]
rs12896900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12896986	0.89[EUR][1000 genomes]
rs14030	0.81[EUR][1000 genomes]
rs17178206	0.89[EUR][1000 genomes]
rs17178234	0.89[EUR][1000 genomes]
rs17178387	0.88[EUR][1000 genomes]
rs17767499	0.86[EUR][1000 genomes]
rs17767523	0.89[EUR][1000 genomes]
rs17767553	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs17767680	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17767686	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1859643	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1981588	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2108049	0.89[EUR][1000 genomes]
rs2108057	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2109276	0.89[EUR][1000 genomes]
rs2190240	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2214836	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2286136	0.93[CHD][hapmap];1.00[JPT][hapmap]
rs2332638	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2332640	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2332641	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2877729	0.88[EUR][1000 genomes]
rs28859432	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs33994051	0.89[EUR][1000 genomes]
rs34169215	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34176710	0.88[EUR][1000 genomes]
rs34281934	0.88[EUR][1000 genomes]
rs34320622	0.89[EUR][1000 genomes]
rs34347034	0.88[EUR][1000 genomes]
rs34388001	0.81[EUR][1000 genomes]
rs34454371	0.88[EUR][1000 genomes]
rs34469007	0.89[EUR][1000 genomes]
rs34480562	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34524083	0.86[EUR][1000 genomes]
rs34528131	0.86[EUR][1000 genomes]
rs34991781	0.80[EUR][1000 genomes]
rs34993988	0.86[EUR][1000 genomes]
rs35051046	0.86[EUR][1000 genomes]
rs35231795	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35415083	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35589413	0.87[EUR][1000 genomes]
rs35609708	0.82[EUR][1000 genomes]
rs35613269	0.89[EUR][1000 genomes]
rs35620527	0.81[EUR][1000 genomes]
rs35680546	0.88[EUR][1000 genomes]
rs35760654	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35831373	0.80[EUR][1000 genomes]
rs35866366	0.81[EUR][1000 genomes]
rs35971049	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs36052007	0.88[EUR][1000 genomes]
rs36072220	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36093218	0.88[EUR][1000 genomes]
rs3784064	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3784066	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3825719	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4140797	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4319698	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4899398	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4902938	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4902941	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4902942	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55883127	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56180634	0.85[EUR][1000 genomes]
rs56407721	0.86[EUR][1000 genomes]
rs61989367	0.89[EUR][1000 genomes]
rs61989373	0.89[EUR][1000 genomes]
rs61989374	0.89[EUR][1000 genomes]
rs61989377	0.88[EUR][1000 genomes]
rs61989379	0.81[EUR][1000 genomes]
rs61989382	0.88[EUR][1000 genomes]
rs61989383	0.93[EUR][1000 genomes]
rs61989386	0.88[EUR][1000 genomes]
rs61989417	0.93[AFR][1000 genomes]
rs61991247	0.86[EUR][1000 genomes]
rs61991248	0.86[EUR][1000 genomes]
rs61991250	0.86[EUR][1000 genomes]
rs61991254	0.85[EUR][1000 genomes]
rs61991255	0.89[EUR][1000 genomes]
rs6574015	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6574016	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66645707	0.88[EUR][1000 genomes]
rs67489015	0.86[EUR][1000 genomes]
rs7140501	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7142343	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7144299	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7144829	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7145755	0.86[EUR][1000 genomes]
rs7147668	0.86[EUR][1000 genomes]
rs7148679	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7152674	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7154787	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7154841	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7156313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7156460	0.86[EUR][1000 genomes]
rs7157241	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs722633	0.89[EUR][1000 genomes]
rs725673	0.89[EUR][1000 genomes]
rs757850	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8003478	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8006300	0.91[CEU][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8008605	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8010616	0.93[EUR][1000 genomes]
rs8013161	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8014349	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8017775	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9323561	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9672060	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[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	nsv498021	chr14:71874708-72128721	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv3398985	chr14:71927884-72404676	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3784062	COQ6	cis	parietal	SCAN
rs3784062	PCNX	cis	parietal	SCAN
rs3784062	SMOC1	cis	cerebellum	SCAN
rs3784062	PCNX	cis	cerebellum	SCAN
rs3784062	SIPA1L1	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:72053400-72098800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr14:72059000-72098600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr14:72072600-72090600	Weak transcription	Fetal Intestine Large	intestine
4	chr14:72072600-72103600	Weak transcription	Left Ventricle	heart
5	chr14:72073200-72090600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr14:72073200-72099200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr14:72073200-72137800	Weak transcription	Esophagus	oesophagus
8	chr14:72073400-72090600	Weak transcription	Pancreas	Pancrea
9	chr14:72073400-72093600	Weak transcription	Gastric	stomach
10	chr14:72073400-72111000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr14:72074000-72090600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr14:72074000-72090600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr14:72075200-72092600	Weak transcription	Brain Substantia Nigra	brain
14	chr14:72075200-72093800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr14:72075200-72106800	Weak transcription	Brain Hippocampus Middle	brain
16	chr14:72077800-72092800	Weak transcription	Fetal Lung	lung
17	chr14:72077800-72096800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr14:72078000-72090600	Weak transcription	Adipose Nuclei	Adipose
19	chr14:72078000-72090600	Weak transcription	Brain Anterior Caudate	brain
20	chr14:72078200-72095800	Weak transcription	Fetal Muscle Leg	muscle
21	chr14:72078600-72100000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr14:72080200-72097000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr14:72080600-72090600	Weak transcription	Ovary	ovary
24	chr14:72081600-72090600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr14:72082600-72125000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr14:72083000-72111000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr14:72083400-72101600	Weak transcription	Fetal Stomach	stomach
28	chr14:72083600-72099000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr14:72083600-72118000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr14:72083600-72128200	Weak transcription	Spleen	Spleen
31	chr14:72083800-72099000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr14:72083800-72099000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr14:72083800-72100400	Weak transcription	Fetal Thymus	thymus
34	chr14:72083800-72105200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr14:72083800-72109800	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr14:72084000-72090800	Weak transcription	Stomach Smooth Muscle	stomach
37	chr14:72084000-72111800	Weak transcription	Thymus	Thymus
38	chr14:72084400-72090600	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr14:72084600-72101400	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr14:72084800-72090600	Weak transcription	Lung	lung
41	chr14:72085000-72090800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr14:72085400-72092800	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr14:72086000-72093000	Strong transcription	Primary B cells from peripheral blood	blood
44	chr14:72086600-72093800	Weak transcription	Primary hematopoietic stem cells	blood
45	chr14:72087000-72090600	Weak transcription	Brain Angular Gyrus	brain
46	chr14:72087200-72095400	Weak transcription	Colon Smooth Muscle	Colon
47	chr14:72087400-72090600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr14:72087400-72090600	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr14:72087400-72091200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr14:72087400-72113400	Weak transcription	Rectal Mucosa Donor 29	rectum

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