Variant report

Variant	rs11718125
Chromosome Location	chr3:52379420-52379421
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52375220..52376808-chr3:52378579..52380565,2	MCF-7	breast:
2	chr3:52378872..52380816-chr3:52409313..52412087,2	MCF-7	breast:
3	chr3:52336627..52339541-chr3:52378479..52380909,2	K562	blood:

Extended variants
information (count: 131 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs1011062	1.00[JPT][hapmap]
rs1011063	1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs1011064	1.00[JPT][hapmap]
rs10460962	0.83[LWK][hapmap]
rs1077142	0.93[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865972	1.00[JPT][hapmap]
rs11705963	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11706001	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11706108	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11707864	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]
rs11707931	0.86[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11709658	0.93[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11710014	0.80[LWK][hapmap]
rs11711934	0.93[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11711974	0.86[LWK][hapmap];0.82[YRI][hapmap]
rs11714402	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715391	0.81[LWK][hapmap]
rs11716017	0.93[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11718729	0.83[AFR][1000 genomes]
rs11721286	1.00[JPT][hapmap]
rs123598	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs123602	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs123603	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs13059674	0.93[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13060192	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs13071708	1.00[JPT][hapmap]
rs13075370	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13076508	1.00[JPT][hapmap]
rs13076890	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13089892	1.00[CHD][hapmap]
rs13091360	1.00[JPT][hapmap]
rs13091545	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1541495	1.00[JPT][hapmap]
rs164637	1.00[JPT][hapmap]
rs17052051	0.83[AFR][1000 genomes]
rs17052052	0.86[LWK][hapmap]
rs17052053	0.86[LWK][hapmap]
rs17052054	0.81[LWK][hapmap]
rs17052058	0.93[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17052061	0.93[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17052068	0.86[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2016575	0.87[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2109558	1.00[JPT][hapmap]
rs2109559	1.00[JPT][hapmap]
rs2159607	0.87[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs2215466	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2335640	0.86[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28481563	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2878549	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs34238085	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34261027	0.83[EUR][1000 genomes]
rs34355561	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34523877	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34551211	1.00[JPT][hapmap]
rs34762015	0.86[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34908451	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35133416	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs352142	1.00[JPT][hapmap]
rs352143	0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs352144	1.00[JPT][hapmap]
rs352173	1.00[JPT][hapmap]
rs353548	1.00[JPT][hapmap]
rs35860312	0.93[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35976326	0.81[AFR][1000 genomes]
rs3733063	0.83[ASW][hapmap];0.88[LWK][hapmap];0.82[AFR][1000 genomes]
rs3752819	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3755810	1.00[CHD][hapmap]
rs3774409	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs3774410	1.00[JPT][hapmap]
rs3796343	0.86[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs390802	0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4082828	0.83[ASW][hapmap];0.83[LWK][hapmap]
rs409803	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs419050	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs419604	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs419752	1.00[CHD][hapmap];1.00[JPT][hapmap]
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]
rs498946	0.93[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55676974	0.81[AFR][1000 genomes]
rs55965068	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55997317	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56357549	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57441156	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59612757	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61150019	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs613519	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs634382	0.93[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs6445386	0.93[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6445486	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6445506	1.00[JPT][hapmap]
rs66462821	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67248391	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs676034	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6763882	0.86[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6771558	1.00[JPT][hapmap]
rs67834575	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6784615	1.00[JPT][hapmap]
rs6793317	0.86[LWK][hapmap]
rs6794675	0.93[EUR][1000 genomes]
rs6796333	0.87[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6800707	0.87[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs6809248	0.80[AFR][1000 genomes]
rs6810027	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs728408	1.00[JPT][hapmap]
rs73088783	0.80[AFR][1000 genomes]
rs73088785	0.83[AFR][1000 genomes]
rs758803	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7620015	1.00[JPT][hapmap]
rs7628461	0.81[LWK][hapmap]
rs7638204	0.81[LWK][hapmap]
rs7643570	0.86[CEU][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs82825	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs887514	1.00[JPT][hapmap]
rs887515	0.87[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs929528	1.00[JPT][hapmap]
rs9844183	0.93[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9846089	1.00[JPT][hapmap]
rs9855470	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9861879	0.95[EUR][1000 genomes];0.92[ASN][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	esv3428292	chr3:52376212-52382310	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11718125	SEMA3G	cis	cerebellum	SCAN
rs11718125	LOC286359	trans	parietal	SCAN
rs11718125	DNAH1	cis	parietal	SCAN
rs11718125	DNAH1	cis	cerebellum	SCAN
rs11718125	PPM1M	cis	parietal	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52352000-52379800	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr3:52352200-52382000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr3:52352200-52384600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr3:52354400-52379800	Weak transcription	Esophagus	oesophagus
5	chr3:52354800-52384000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr3:52358400-52380400	Weak transcription	Ovary	ovary
7	chr3:52364200-52383000	Weak transcription	Fetal Lung	lung
8	chr3:52364800-52394400	Weak transcription	HSMMtube	muscle
9	chr3:52366400-52383000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:52366600-52386600	Weak transcription	Aorta	Aorta
11	chr3:52366800-52383000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr3:52367200-52379600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr3:52367600-52384400	Weak transcription	Fetal Kidney	kidney
14	chr3:52368400-52383000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr3:52368800-52380200	Weak transcription	Left Ventricle	heart
16	chr3:52368800-52380400	Weak transcription	Placenta	Placenta
17	chr3:52368800-52380400	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr3:52370600-52379600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr3:52372000-52379600	Weak transcription	NHLF	lung
20	chr3:52372000-52380400	Weak transcription	Primary hematopoietic stem cells	blood
21	chr3:52372200-52379600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:52372600-52379600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:52372600-52379600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:52373800-52396000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr3:52374000-52382200	Weak transcription	Brain Germinal Matrix	brain
26	chr3:52374000-52385400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr3:52374000-52386200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:52374000-52399000	Weak transcription	Stomach Mucosa	stomach
29	chr3:52374000-52407000	Strong transcription	Fetal Intestine Small	intestine
30	chr3:52374200-52427000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr3:52375400-52405600	Strong transcription	Lung	lung
32	chr3:52375800-52381000	Strong transcription	Fetal Stomach	stomach
33	chr3:52376400-52402000	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr3:52376800-52384400	Weak transcription	GM12878-XiMat	blood
35	chr3:52377000-52406600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr3:52377000-52406600	Strong transcription	Liver	Liver
37	chr3:52377200-52390600	Strong transcription	Primary T cells from cord blood	blood
38	chr3:52377200-52405200	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr3:52377400-52379600	Strong transcription	Fetal Muscle Leg	muscle
40	chr3:52377400-52380400	Strong transcription	Adipose Nuclei	Adipose
41	chr3:52377400-52382400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr3:52377400-52384600	Strong transcription	Duodenum Mucosa	Duodenum
43	chr3:52377400-52397400	Strong transcription	Brain Inferior Temporal Lobe	brain
44	chr3:52377400-52404800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:52377400-52406600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr3:52377400-52406800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr3:52377600-52380400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr3:52377600-52384000	Weak transcription	Fetal Thymus	thymus
49	chr3:52377600-52406200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr3:52377800-52380000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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