Variant report

Variant	rs9409660
Chromosome Location	chr9:94998242-94998243
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	chr9:94995085..94999112-chr9:95010156..95013244,4	K562	blood:
2	chr9:94996019..94998973-chr9:95056165..95057730,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196305	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10125510	0.93[CEU][hapmap];0.91[EUR][1000 genomes]
rs1058726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1058751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10733744	0.93[CEU][hapmap];0.91[EUR][1000 genomes]
rs10761159	0.91[EUR][1000 genomes]
rs1144933	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1152760	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1152761	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1152762	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1175737	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1175923	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1175929	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1175930	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1175931	0.88[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11787696	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11788610	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11789578	0.91[CHB][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11790257	0.82[CHB][hapmap];0.85[ASN][1000 genomes]
rs11791931	0.93[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11792542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11793505	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11794966	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12555097	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2084289	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2295939	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2398749	0.85[EUR][1000 genomes]
rs2761680	0.93[CEU][hapmap];0.91[EUR][1000 genomes]
rs3894058	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs41280213	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41280215	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs472163	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4743862	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4743864	0.85[ASN][1000 genomes]
rs4743866	0.87[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4743867	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4743868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743871	0.92[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4744123	0.85[ASN][1000 genomes]
rs4744124	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs501814	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs556155	0.87[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs557066	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55894730	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56110031	0.85[ASN][1000 genomes]
rs56308715	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs56374228	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6479421	0.93[CEU][hapmap];0.91[EUR][1000 genomes]
rs7042199	0.91[EUR][1000 genomes]
rs72748400	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs72748402	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7864453	0.91[EUR][1000 genomes]
rs895639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9409464	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9409465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9409466	0.88[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9409467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9409469	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9409659	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9409661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9409662	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9409663	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9409665	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9409666	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs944949	0.93[CEU][hapmap];0.91[EUR][1000 genomes]

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	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530947	chr9:94697309-95093377	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv917089	chr9:94857047-95099848	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv893573	chr9:94974188-95355719	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94974000-94999000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:94982800-95038400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr9:94982800-95045600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr9:94984000-95012400	Weak transcription	Stomach Mucosa	stomach
5	chr9:94985200-95001000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr9:94986000-95000600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr9:94988400-95000800	Weak transcription	Aorta	Aorta
8	chr9:94988800-95000400	Weak transcription	Fetal Heart	heart
9	chr9:94990200-95003200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr9:94990200-95003200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr9:94990200-95004200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr9:94990200-95054000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr9:94990400-95004000	Strong transcription	Osteobl	bone
14	chr9:94990400-95004200	Strong transcription	NH-A	brain
15	chr9:94990400-95038200	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr9:94990600-95004000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr9:94991000-95000400	Weak transcription	Colonic Mucosa	Colon
18	chr9:94991000-95007000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr9:94991200-95000400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr9:94991200-95000400	Weak transcription	Pancreas	Pancrea
21	chr9:94991200-95002000	Weak transcription	Small Intestine	intestine
22	chr9:94991200-95006600	Strong transcription	HMEC	breast
23	chr9:94991200-95038400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr9:94991200-95052400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr9:94991200-95053600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr9:94991400-94998600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr9:94991400-94998800	Weak transcription	Ovary	ovary
28	chr9:94991400-94999000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr9:94991400-94999200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr9:94991400-94999200	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr9:94991400-94999400	Weak transcription	Brain Cingulate Gyrus	brain
32	chr9:94991400-94999800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr9:94991400-94999800	Weak transcription	Colon Smooth Muscle	Colon
34	chr9:94991400-95000000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr9:94991400-95000200	Weak transcription	Right Ventricle	heart
36	chr9:94991400-95000400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr9:94991400-95000400	Weak transcription	Brain Substantia Nigra	brain
38	chr9:94991400-95000400	Weak transcription	Rectal Smooth Muscle	rectum
39	chr9:94991400-95000400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr9:94991400-95000600	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr9:94991400-95000600	Weak transcription	Brain Angular Gyrus	brain
42	chr9:94991400-95000600	Weak transcription	Fetal Kidney	kidney
43	chr9:94991400-95000600	Weak transcription	Placenta	Placenta
44	chr9:94991400-95000800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr9:94991400-95001400	Weak transcription	Brain Germinal Matrix	brain
46	chr9:94991400-95004000	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr9:94991400-95050400	Strong transcription	Dnd41	blood
48	chr9:94991400-95052400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr9:94991400-95053600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr9:94991400-95053800	Strong transcription	HUES48 Cell Line	embryonic stem cell

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