Variant report

Variant	rs10992393
Chromosome Location	chr9:95420983-95420984
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	chr9:95415511..95417120-chr9:95418823..95421192,2	MCF-7	breast:

Extended variants
information (count: 79 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10114912	0.81[EUR][1000 genomes]
rs10114932	0.80[EUR][1000 genomes]
rs10116241	0.83[CEU][hapmap]
rs10118939	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs10122383	0.95[CEU][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10124058	0.88[EUR][1000 genomes]
rs10125587	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs1022844	0.91[CEU][hapmap]
rs10429459	0.87[CEU][hapmap]
rs10491804	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10514815	0.87[CEU][hapmap]
rs10761163	0.81[EUR][1000 genomes]
rs10761164	0.84[CEU][hapmap]
rs10820980	0.95[CEU][hapmap]
rs10820986	0.80[CEU][hapmap]
rs10820990	0.80[CEU][hapmap]
rs10820994	0.85[EUR][1000 genomes]
rs10821008	0.91[CEU][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs10992349	0.95[CEU][hapmap]
rs10992366	0.81[EUR][1000 genomes]
rs10992424	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10992450	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10992457	0.88[EUR][1000 genomes]
rs11794346	0.95[CEU][hapmap];0.84[TSI][hapmap]
rs12338938	0.83[CEU][hapmap]
rs12341817	0.95[CEU][hapmap];0.84[TSI][hapmap]
rs12343820	0.91[CEU][hapmap]
rs13284106	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13286566	0.88[EUR][1000 genomes]
rs13301537	0.95[CEU][hapmap];0.84[TSI][hapmap]
rs1980848	0.95[CEU][hapmap];0.84[TSI][hapmap]
rs2026585	0.84[CEU][hapmap]
rs2094281	0.95[CEU][hapmap];0.90[TSI][hapmap]
rs2104533	0.84[CEU][hapmap]
rs2181585	0.86[CEU][hapmap]
rs2296666	0.87[CEU][hapmap]
rs2296667	0.84[CEU][hapmap]
rs2296669	0.95[CEU][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs2895219	0.84[CEU][hapmap]
rs3739606	0.87[CEU][hapmap]
rs4743873	0.95[CEU][hapmap];0.84[TSI][hapmap]
rs4743874	0.83[CEU][hapmap]
rs4743875	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4743876	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4744133	0.87[CEU][hapmap]
rs4744134	0.84[CEU][hapmap]
rs4744135	0.87[CEU][hapmap]
rs4744136	0.84[CEU][hapmap]
rs4744137	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs4744138	0.91[CEU][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes]
rs4744141	0.95[CEU][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs4744143	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6479431	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7020104	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7029939	0.81[EUR][1000 genomes]
rs7031567	0.87[CEU][hapmap]
rs7033979	0.95[CEU][hapmap]
rs7043984	0.91[CEU][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs7046335	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs724102	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs747628	0.80[EUR][1000 genomes]
rs747629	0.84[CEU][hapmap]
rs755209	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7847534	0.80[EUR][1000 genomes]
rs7848391	0.80[CEU][hapmap]
rs7852698	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7860786	0.87[CEU][hapmap]
rs7864575	0.95[CEU][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes]
rs7864630	0.84[CEU][hapmap]
rs7865019	0.95[CEU][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes]
rs7865118	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7868013	0.95[CEU][hapmap];0.83[TSI][hapmap]
rs7869521	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7869742	0.84[CEU][hapmap]
rs7872610	0.80[EUR][1000 genomes]
rs927865	0.87[CEU][hapmap]
rs9299405	0.95[CEU][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes]
rs968040	0.95[CEU][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes]
rs987553	0.80[EUR][1000 genomes]

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10992393	CENPP	cis	Esophagus Muscularis	GTEx
rs10992393	CENPP	cis	parietal	SCAN
rs10992393	ZNF484	cis	parietal	SCAN
rs10992393	NOL8	cis	cerebellum	SCAN
rs10992393	CENPP	cis	cerebellum	SCAN
rs10992393	RP11-19J3.3	cis	multi-tissue	Pritchard
rs10992393	ZNF484	cis	cerebellum	SCAN
rs10992393	CENPP	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95373000-95421200	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr9:95380800-95429000	Weak transcription	Stomach Mucosa	stomach
3	chr9:95384800-95421600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr9:95391800-95421000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr9:95393200-95421200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr9:95393200-95421600	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr9:95393600-95421000	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr9:95393800-95421000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr9:95396800-95422400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr9:95401200-95421800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr9:95401200-95422000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:95408400-95421200	Strong transcription	Brain Germinal Matrix	brain
13	chr9:95408800-95421000	Strong transcription	Thymus	Thymus
14	chr9:95408800-95426800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr9:95409600-95421200	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr9:95409800-95431000	Weak transcription	Fetal Kidney	kidney
17	chr9:95410800-95427000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr9:95411000-95431400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr9:95411400-95421800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr9:95411800-95426600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr9:95411800-95427400	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr9:95412000-95422000	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr9:95412000-95422000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr9:95412000-95423800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr9:95412000-95426600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr9:95412000-95428400	Weak transcription	K562	blood
27	chr9:95412000-95431000	Weak transcription	Fetal Brain Male	brain
28	chr9:95412400-95431200	Weak transcription	Small Intestine	intestine
29	chr9:95413400-95427000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr9:95414000-95421200	Strong transcription	Fetal Stomach	stomach
31	chr9:95415200-95421000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr9:95415200-95422000	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr9:95415400-95421200	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr9:95415400-95421200	Strong transcription	Fetal Thymus	thymus
35	chr9:95416000-95421200	Strong transcription	Brain Anterior Caudate	brain
36	chr9:95416000-95421400	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr9:95416200-95421400	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr9:95416200-95421400	Strong transcription	Dnd41	blood
39	chr9:95416400-95421000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr9:95416800-95426600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr9:95417000-95421200	Genic enhancers	Spleen	Spleen
42	chr9:95417200-95421200	Strong transcription	HUVEC	blood vessel
43	chr9:95417400-95421200	Strong transcription	Brain Inferior Temporal Lobe	brain
44	chr9:95417400-95421200	Strong transcription	Stomach Smooth Muscle	stomach
45	chr9:95417600-95422000	Strong transcription	Primary B cells from peripheral blood	blood
46	chr9:95417600-95422400	Weak transcription	NH-A	brain
47	chr9:95417800-95421200	Strong transcription	GM12878-XiMat	blood
48	chr9:95417800-95421400	Strong transcription	A549	lung
49	chr9:95417800-95426600	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr9:95417800-95426600	Weak transcription	Right Atrium	heart

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