Variant report

Variant	rs11707864
Chromosome Location	chr3:52392877-52392878
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52391704..52393563-chr3:52402367..52404938,2	MCF-7	breast:

Extended variants
information (count: 139 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:134)

rs_ID	r²[population]
rs1011062	1.00[JPT][hapmap]
rs1011063	1.00[JPT][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.81[YRI][hapmap]
rs1011064	1.00[JPT][hapmap]
rs10460962	0.86[LWK][hapmap]
rs1077142	0.86[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs10865972	1.00[JPT][hapmap]
rs11705963	0.92[EUR][1000 genomes]
rs11706001	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11706108	0.92[EUR][1000 genomes]
rs11707931	0.93[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709658	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11710014	0.83[LWK][hapmap]
rs11711934	0.83[ASW][hapmap];0.86[CEU][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs11711974	0.89[LWK][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes]
rs11714402	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11716017	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11718125	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11721277	0.81[AFR][1000 genomes]
rs11721286	1.00[JPT][hapmap]
rs123598	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs123602	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs123603	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13059674	0.83[ASW][hapmap];0.86[CEU][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.82[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs13060192	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13071708	1.00[JPT][hapmap]
rs13075370	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13076508	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13076890	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13089892	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs13091360	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13091545	0.93[CEU][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs13096571	1.00[ASN][1000 genomes]
rs1541495	1.00[JPT][hapmap]
rs164637	1.00[JPT][hapmap]
rs17052052	0.83[LWK][hapmap]
rs17052053	0.89[LWK][hapmap]
rs17052054	0.83[LWK][hapmap]
rs17052058	0.83[ASW][hapmap];0.86[CEU][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.81[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs17052061	0.83[ASW][hapmap];0.86[CEU][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap];0.81[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs17052068	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2016575	0.82[ASW][hapmap];0.86[CEU][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.82[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.86[EUR][1000 genomes]
rs2109557	1.00[ASN][1000 genomes]
rs2109558	1.00[JPT][hapmap]
rs2109559	1.00[JPT][hapmap]
rs2159607	0.80[CEU][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.81[YRI][hapmap]
rs2215466	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2335640	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28481563	0.92[EUR][1000 genomes]
rs2878549	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34181173	1.00[ASN][1000 genomes]
rs34238085	0.82[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs34261027	0.80[EUR][1000 genomes]
rs34332947	1.00[ASN][1000 genomes]
rs34355561	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34523877	0.82[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs34551211	1.00[JPT][hapmap]
rs34628357	1.00[ASN][1000 genomes]
rs34762015	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34827613	1.00[ASN][1000 genomes]
rs34908451	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35133416	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs352142	1.00[JPT][hapmap]
rs352143	1.00[JPT][hapmap]
rs352144	1.00[JPT][hapmap]
rs352173	1.00[JPT][hapmap]
rs353548	1.00[JPT][hapmap]
rs35860312	0.86[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs35982798	1.00[ASN][1000 genomes]
rs3733063	0.85[LWK][hapmap]
rs3752819	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3755810	1.00[CHD][hapmap]
rs3774409	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs3774410	1.00[JPT][hapmap]
rs3796343	1.00[JPT][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs390802	0.86[CEU][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs4082828	0.80[LWK][hapmap]
rs409803	1.00[JPT][hapmap]
rs419050	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs419604	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs419752	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4312651	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4687614	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4687617	1.00[JPT][hapmap]
rs4687618	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4687619	1.00[JPT][hapmap]
rs498778	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs498946	0.86[CEU][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs55965068	0.94[EUR][1000 genomes]
rs55997317	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs56322342	0.80[AFR][1000 genomes]
rs56357549	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56899118	0.85[AFR][1000 genomes]
rs57441156	0.94[EUR][1000 genomes]
rs575476	1.00[ASN][1000 genomes]
rs59612757	0.91[EUR][1000 genomes]
rs61150019	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs613519	1.00[JPT][hapmap]
rs61734640	1.00[ASN][1000 genomes]
rs634382	0.86[CEU][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs6445386	0.83[ASW][hapmap];0.86[CEU][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.81[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs6445486	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6445506	1.00[JPT][hapmap]
rs66462821	0.93[EUR][1000 genomes]
rs67248391	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs676034	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6763882	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6771558	1.00[JPT][hapmap]
rs67834575	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784615	1.00[JPT][hapmap]
rs6793317	0.83[LWK][hapmap]
rs6794675	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6795333	1.00[ASN][1000 genomes]
rs6796333	0.83[ASW][hapmap];0.80[CEU][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs6800707	0.80[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs6810027	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs71297391	1.00[ASN][1000 genomes]
rs71297394	1.00[ASN][1000 genomes]
rs71297395	1.00[ASN][1000 genomes]
rs71297396	1.00[ASN][1000 genomes]
rs728408	1.00[JPT][hapmap]
rs73091168	0.85[AFR][1000 genomes]
rs758803	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7620015	1.00[JPT][hapmap]
rs7643570	0.81[MEX][hapmap];0.83[TSI][hapmap];0.93[EUR][1000 genomes]
rs82825	0.92[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[EUR][1000 genomes]
rs887514	1.00[JPT][hapmap]
rs887515	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs929528	1.00[JPT][hapmap]
rs9844183	0.85[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs9846089	1.00[JPT][hapmap]
rs9855470	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9861879	0.92[EUR][1000 genomes]
rs9863753	1.00[JPT][hapmap]
rs9867823	1.00[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases
2	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
3	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
4	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	45 gene(s)	inside rSNPs	diseases
5	nsv979833	chr3:52387550-52407592	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11707864	SEMA3G	cis	cerebellum	SCAN
rs11707864	DNAH1	cis	cerebellum	SCAN
rs11707864	DNAH1	cis	parietal	SCAN
rs11707864	LOC286359	trans	parietal	SCAN
rs11707864	ITIH3	cis	parietal	SCAN
rs11707864	PPM1M	cis	parietal	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52364800-52394400	Weak transcription	HSMMtube	muscle
2	chr3:52373800-52396000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr3:52374000-52399000	Weak transcription	Stomach Mucosa	stomach
4	chr3:52374000-52407000	Strong transcription	Fetal Intestine Small	intestine
5	chr3:52374200-52427000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr3:52375400-52405600	Strong transcription	Lung	lung
7	chr3:52376400-52402000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:52377000-52406600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:52377000-52406600	Strong transcription	Liver	Liver
10	chr3:52377200-52405200	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr3:52377400-52397400	Strong transcription	Brain Inferior Temporal Lobe	brain
12	chr3:52377400-52404800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:52377400-52406600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr3:52377400-52406800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr3:52377600-52406200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr3:52377800-52406200	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr3:52377800-52407200	Strong transcription	Fetal Intestine Large	intestine
18	chr3:52378400-52400000	Strong transcription	Brain Anterior Caudate	brain
19	chr3:52378400-52401200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr3:52378400-52401200	Strong transcription	Gastric	stomach
21	chr3:52378400-52401800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr3:52378600-52400000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:52378600-52400200	Strong transcription	Brain Cingulate Gyrus	brain
24	chr3:52378600-52400200	Strong transcription	Brain Hippocampus Middle	brain
25	chr3:52378600-52405000	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr3:52378600-52406800	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr3:52379400-52410600	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr3:52380400-52401000	Strong transcription	Placenta	Placenta
29	chr3:52380800-52396400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr3:52381400-52401200	Strong transcription	Ovary	ovary
31	chr3:52381400-52402600	Strong transcription	Fetal Stomach	stomach
32	chr3:52381400-52404200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr3:52381400-52407400	Weak transcription	NHLF	lung
34	chr3:52381600-52396400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr3:52381600-52397600	Strong transcription	Stomach Smooth Muscle	stomach
36	chr3:52381600-52405400	Strong transcription	Adipose Nuclei	Adipose
37	chr3:52381600-52405800	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr3:52381800-52397000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:52382200-52395800	Weak transcription	Psoas Muscle	Psoas
40	chr3:52382400-52396000	Strong transcription	Colonic Mucosa	Colon
41	chr3:52383000-52401400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr3:52383600-52394000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr3:52383600-52394000	Weak transcription	Rectal Smooth Muscle	rectum
44	chr3:52384000-52394400	Weak transcription	Fetal Lung	lung
45	chr3:52384000-52395400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr3:52384600-52406200	Weak transcription	GM12878-XiMat	blood
47	chr3:52385400-52398400	Strong transcription	Fetal Muscle Leg	muscle
48	chr3:52385400-52434600	Weak transcription	Small Intestine	intestine
49	chr3:52385800-52394000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr3:52385800-52395800	Strong transcription	Fetal Muscle Trunk	muscle

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