Variant report

Variant	rs17519385
Chromosome Location	chr1:92676309-92676310
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:92674870..92677201-chr1:92679894..92682491,3	MCF-7	breast:

Extended variants
information (count: 168 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:162)

rs_ID	r²[population]
rs1014415	1.00[JPT][hapmap]
rs10159094	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs1023041	1.00[JPT][hapmap]
rs10874637	0.83[ASN][1000 genomes]
rs10875209	1.00[JPT][hapmap]
rs10875214	1.00[JPT][hapmap]
rs10875237	0.80[EUR][1000 genomes]
rs10875319	1.00[JPT][hapmap]
rs10875349	1.00[JPT][hapmap]
rs11164226	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11164288	1.00[JPT][hapmap]
rs11164312	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11165984	1.00[JPT][hapmap]
rs11166042	1.00[JPT][hapmap]
rs11166141	1.00[JPT][hapmap]
rs11166144	1.00[JPT][hapmap]
rs1157469	0.88[TSI][hapmap]
rs1157470	1.00[JPT][hapmap]
rs11577572	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11577839	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11578012	0.89[ASN][1000 genomes]
rs11578400	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11580693	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11585255	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11586355	0.82[EUR][1000 genomes]
rs11586989	0.82[EUR][1000 genomes]
rs11588044	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11588153	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11589858	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11803457	1.00[JPT][hapmap]
rs12094293	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12119246	1.00[JPT][hapmap]
rs1226176	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1226179	0.83[EUR][1000 genomes]
rs1226183	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1226187	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12401372	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12404806	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12406749	0.88[EUR][1000 genomes]
rs12407622	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12411162	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12724638	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12727665	0.89[ASN][1000 genomes]
rs12729867	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap]
rs12731923	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12734478	0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap]
rs12735898	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12740246	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs12749317	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12753920	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12755781	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12757533	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12759512	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1384612	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1384613	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1483022	0.83[CEU][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs1487536	1.00[JPT][hapmap]
rs1487540	1.00[JPT][hapmap]
rs1542685	1.00[JPT][hapmap]
rs17519972	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17578686	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1809606	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1872007	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1982720	1.00[JPT][hapmap]
rs2004814	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2046620	1.00[JPT][hapmap]
rs2069051	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2087194	1.00[JPT][hapmap]
rs2093879	1.00[JPT][hapmap]
rs2128645	1.00[JPT][hapmap]
rs2128646	1.00[JPT][hapmap]
rs2181897	0.85[EUR][1000 genomes]
rs2391114	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs2391158	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2391162	0.89[ASN][1000 genomes]
rs2839877	1.00[JPT][hapmap]
rs2893200	1.00[JPT][hapmap];0.88[TSI][hapmap]
rs3103176	1.00[JPT][hapmap]
rs3103178	1.00[JPT][hapmap]
rs3103181	1.00[JPT][hapmap]
rs3131814	1.00[JPT][hapmap]
rs3131828	1.00[JPT][hapmap]
rs34090353	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35015161	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35580949	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3851271	1.00[JPT][hapmap];0.88[TSI][hapmap]
rs3851272	1.00[JPT][hapmap];0.88[TSI][hapmap]
rs3851273	1.00[JPT][hapmap]
rs4437922	1.00[JPT][hapmap]
rs4658128	1.00[JPT][hapmap]
rs4658290	1.00[JPT][hapmap]
rs4658294	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4658297	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4658298	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4658299	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4658300	1.00[JPT][hapmap]
rs488288	0.81[EUR][1000 genomes]
rs488849	1.00[JPT][hapmap]
rs490800	0.83[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs492164	0.87[CEU][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs493595	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs4949888	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4970699	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4970713	0.89[ASN][1000 genomes]
rs504606	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs504613	0.82[EUR][1000 genomes]
rs506375	0.87[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs506377	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs507452	1.00[JPT][hapmap]
rs511546	0.82[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs515280	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs519343	0.81[EUR][1000 genomes]
rs519623	0.82[EUR][1000 genomes]
rs519932	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs527412	0.83[CEU][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs529135	1.00[JPT][hapmap]
rs534547	1.00[JPT][hapmap]
rs539288	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs544557	0.85[EUR][1000 genomes]
rs547699	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs551909	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs553861	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs556980	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs560389	0.91[CEU][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs563113	0.87[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs563606	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs564971	0.84[EUR][1000 genomes]
rs569593	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs570368	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs573044	0.87[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs575805	0.87[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs58394161	0.83[ASN][1000 genomes]
rs6603962	1.00[JPT][hapmap]
rs6603973	0.83[ASN][1000 genomes]
rs6603974	0.83[ASN][1000 genomes]
rs6604080	1.00[JPT][hapmap]
rs6604082	0.83[CEU][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs6604090	1.00[JPT][hapmap]
rs6662379	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6663278	1.00[JPT][hapmap]
rs6663905	0.89[ASN][1000 genomes]
rs6668803	1.00[JPT][hapmap]
rs66758257	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6684317	1.00[JPT][hapmap]
rs6699855	1.00[JPT][hapmap]
rs6702267	1.00[JPT][hapmap]
rs72720457	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7511656	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7511669	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7517541	1.00[JPT][hapmap]
rs7520275	1.00[JPT][hapmap]
rs7522081	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7524120	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7533077	1.00[JPT][hapmap];0.87[TSI][hapmap]
rs7537221	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7542358	1.00[JPT][hapmap]
rs7542373	1.00[JPT][hapmap]
rs7543947	1.00[JPT][hapmap]
rs7545076	0.87[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs7550680	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9439911	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs981583	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv530438	chr1:92091957-92827760	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv530046	chr1:92277460-92799794	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv871508	chr1:92478130-92781579	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv830592	chr1:92669282-92805629	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17519385	ZNF326	cis	cerebellum	SCAN
rs17519385	MT1DP	trans	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92674800-92676800	Enhancers	Primary T cells from cord blood	blood
2	chr1:92675200-92677000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr1:92675400-92676800	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr1:92675400-92676800	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr1:92675600-92677000	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr1:92676000-92676600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:92676000-92676600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:92676000-92676800	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr1:92676000-92676800	Enhancers	Dnd41	blood
10	chr1:92676200-92676400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:92676200-92676600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr1:92676200-92676600	Enhancers	Aorta	Aorta
13	chr1:92676200-92676600	Enhancers	Thymus	Thymus
14	chr1:92676200-92676600	Enhancers	HMEC	breast
15	chr1:92676200-92676600	Enhancers	NH-A	brain
16	chr1:92676200-92676800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:92676200-92676800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:92676200-92676800	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr1:92676200-92676800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
20	chr1:92676200-92676800	Flanking Active TSS	Osteobl	bone
21	chr1:92676200-92677000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:92676200-92677000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr1:92676200-92677000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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