Variant report

Variant	rs2296669
Chromosome Location	chr9:95373790-95373791
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	chr9:95373177..95375110-chr9:95377702..95380287,2	MCF-7	breast:

Extended variants
information (count: 110 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10114912	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10114932	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10116241	0.87[CEU][hapmap];0.80[MEX][hapmap]
rs10118939	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10122383	0.91[CEU][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs10124058	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10125587	0.96[CEU][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1022844	0.87[CEU][hapmap]
rs10429459	0.91[CEU][hapmap]
rs10453241	0.88[CEU][hapmap]
rs10491804	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs10514815	0.91[CEU][hapmap];0.80[MEX][hapmap]
rs10761158	0.91[CEU][hapmap];0.80[MEX][hapmap]
rs10761160	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10761163	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10761164	0.88[CEU][hapmap]
rs10820980	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10820986	0.84[CEU][hapmap]
rs10820990	0.84[CEU][hapmap]
rs10820994	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10821008	0.82[ASW][hapmap];0.96[CEU][hapmap];0.89[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10992347	0.91[CEU][hapmap]
rs10992349	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10992366	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10992393	0.95[CEU][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs10992424	0.86[EUR][1000 genomes]
rs10992450	0.84[EUR][1000 genomes]
rs10992457	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11788511	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs11788523	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11791339	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap]
rs11792019	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11793563	0.93[ASN][1000 genomes]
rs11794346	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12336415	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12338938	0.87[CEU][hapmap]
rs12341817	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12342019	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12343820	0.87[CEU][hapmap]
rs13284106	0.90[EUR][1000 genomes]
rs13286566	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13301537	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1535754	0.91[CEU][hapmap];0.80[MEX][hapmap]
rs1535756	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap]
rs1980848	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2026585	0.88[CEU][hapmap]
rs2094281	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2104533	0.83[ASW][hapmap];0.88[CEU][hapmap]
rs2181585	0.81[CEU][hapmap]
rs2296666	0.91[CEU][hapmap];0.80[MEX][hapmap]
rs2296667	0.88[CEU][hapmap]
rs2296670	1.00[ASN][1000 genomes]
rs2516567	0.88[CEU][hapmap];0.80[MEX][hapmap]
rs2516568	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2761677	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2761678	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs2761681	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap]
rs2895219	0.83[ASW][hapmap];0.88[CEU][hapmap]
rs3739606	0.91[CEU][hapmap];0.80[MEX][hapmap]
rs4743873	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4743874	0.87[CEU][hapmap]
rs4743875	0.95[CEU][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs4743876	0.86[EUR][1000 genomes]
rs4744133	0.91[CEU][hapmap];0.80[MEX][hapmap]
rs4744134	0.88[CEU][hapmap];0.80[MEX][hapmap]
rs4744135	0.91[CEU][hapmap];0.80[MEX][hapmap]
rs4744136	0.88[CEU][hapmap];0.80[MEX][hapmap]
rs4744137	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4744138	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4744141	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4744143	0.91[EUR][1000 genomes]
rs62572543	0.84[EUR][1000 genomes]
rs6479422	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6479431	0.85[EUR][1000 genomes]
rs7020104	0.95[CEU][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs7022562	0.91[CEU][hapmap];0.80[MEX][hapmap]
rs7029939	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7031567	0.91[CEU][hapmap];0.80[MEX][hapmap]
rs7033333	0.98[ASN][1000 genomes]
rs7033979	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7037075	0.88[CEU][hapmap];0.80[MEX][hapmap]
rs7037194	0.91[CEU][hapmap];0.80[MEX][hapmap]
rs7043984	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7045409	0.88[CEU][hapmap];0.80[MEX][hapmap]
rs7046335	0.82[EUR][1000 genomes]
rs724102	0.91[CEU][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes]
rs747628	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs747629	0.88[CEU][hapmap]
rs755209	0.86[EUR][1000 genomes]
rs7847534	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7848391	0.84[CEU][hapmap]
rs7848399	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs7848472	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap]
rs7850528	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7852698	0.95[CEU][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs7860786	0.91[CEU][hapmap];0.80[MEX][hapmap]
rs7864575	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7864630	0.88[CEU][hapmap];0.80[MEX][hapmap]
rs7865019	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7865118	0.91[EUR][1000 genomes]
rs7868013	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7869521	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs7869742	0.88[CEU][hapmap];0.80[MEX][hapmap]
rs7872610	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7873397	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8067	0.88[CEU][hapmap]
rs927865	0.91[CEU][hapmap];0.80[MEX][hapmap]
rs9299405	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs968040	0.83[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.80[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs987553	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2296669	CENPP	cis	parietal	SCAN
rs2296669	CENPP	cis	Esophagus Muscularis	GTEx
rs2296669	NOL8	cis	cerebellum	SCAN
rs2296669	ZNF484	cis	cerebellum	SCAN
rs2296669	CENPP	cis	cerebellum	SCAN
rs2296669	RP11-19J3.3	cis	multi-tissue	Pritchard
rs2296669	ZNF484	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95363400-95374000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:95363400-95396000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr9:95366400-95375000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr9:95367400-95373800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr9:95367400-95380600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr9:95369400-95373800	Enhancers	NHDF-Ad	bronchial
7	chr9:95369800-95374200	Weak transcription	Liver	Liver
8	chr9:95369800-95374200	Weak transcription	GM12878-XiMat	blood
9	chr9:95370200-95376200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr9:95370600-95394000	Weak transcription	Psoas Muscle	Psoas
11	chr9:95370800-95373800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr9:95370800-95374200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr9:95370800-95377800	Weak transcription	Fetal Brain Male	brain
14	chr9:95370800-95380400	Weak transcription	Fetal Heart	heart
15	chr9:95371000-95373800	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr9:95371200-95375200	Weak transcription	NH-A	brain
17	chr9:95371200-95379800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr9:95371400-95373800	Genic enhancers	NHLF	lung
19	chr9:95371400-95398200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr9:95371600-95373800	Weak transcription	Osteobl	bone
21	chr9:95371600-95374000	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr9:95371800-95374000	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr9:95371800-95374000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr9:95371800-95374000	Weak transcription	Pancreas	Pancrea
25	chr9:95371800-95374200	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr9:95371800-95376000	Weak transcription	Brain Angular Gyrus	brain
27	chr9:95371800-95377000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr9:95371800-95377400	Weak transcription	Fetal Kidney	kidney
29	chr9:95371800-95377600	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr9:95371800-95379800	Weak transcription	Stomach Mucosa	stomach
31	chr9:95371800-95382400	Weak transcription	Right Atrium	heart
32	chr9:95371800-95399000	Weak transcription	Aorta	Aorta
33	chr9:95371800-95407400	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr9:95372000-95374000	Weak transcription	Primary B cells from peripheral blood	blood
35	chr9:95372000-95374000	Weak transcription	Colonic Mucosa	Colon
36	chr9:95372000-95374200	Weak transcription	Rectal Smooth Muscle	rectum
37	chr9:95372000-95380200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr9:95372000-95394200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr9:95372200-95373800	Weak transcription	HepG2	liver
40	chr9:95372200-95374000	Weak transcription	Primary B cells from cord blood	blood
41	chr9:95372200-95375400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr9:95372200-95380400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr9:95372400-95373800	Enhancers	Muscle Satellite Cultured Cells	--
44	chr9:95372400-95374400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr9:95372400-95383400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr9:95372600-95374200	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr9:95372600-95374400	Enhancers	HSMMtube	muscle
48	chr9:95372600-95381400	Genic enhancers	Fetal Stomach	stomach
49	chr9:95372600-95383200	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr9:95372800-95373800	Genic enhancers	Rectal Mucosa Donor 29	rectum

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