Variant report

Variant	rs7020104
Chromosome Location	chr9:95416524-95416525
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:95401673..95403415-chr9:95415662..95417895,2	K562	blood:
2	chr9:95415511..95417120-chr9:95418823..95421192,2	MCF-7	breast:
3	chr9:95415723..95417992-chr9:95421867..95424824,2	K562	blood:
4	chr9:95410388..95412168-chr9:95415028..95416964,2	MCF-7	breast:
5	chr9:95400830..95403415-chr9:95415662..95417895,3	K562	blood:
6	chr9:95415301..95417414-chr9:95526499..95528490,2	MCF-7	breast:
7	chr9:95415028..95419366-chr9:95430652..95433833,9	MCF-7	breast:
8	chr9:95416446..95420766-chr9:95422078..95429343,12	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000185963	Chromatin interaction
ENSG00000127080	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10114912	0.81[EUR][1000 genomes]
rs10116241	0.83[CEU][hapmap]
rs10118939	0.95[CEU][hapmap]
rs10122383	0.95[CEU][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10124058	0.87[EUR][1000 genomes]
rs10125587	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs1022844	0.91[CEU][hapmap]
rs10429459	0.87[CEU][hapmap]
rs10491804	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.93[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	0.84[EUR][1000 genomes]
rs10820995	0.91[LWK][hapmap];0.80[MKK][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes]
rs10820999	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10821008	0.91[CEU][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs10992347	0.87[CEU][hapmap]
rs10992349	0.95[CEU][hapmap]
rs10992366	0.81[EUR][1000 genomes]
rs10992393	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]
rs10992424	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10992450	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10992457	0.87[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	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13286566	0.87[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];0.91[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[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4743876	0.87[AMR][1000 genomes];0.93[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]
rs4744138	0.91[CEU][hapmap];0.90[TSI][hapmap]
rs4744141	0.95[CEU][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs4744143	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6479431	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7029939	0.81[EUR][1000 genomes]
rs7031567	0.87[CEU][hapmap]
rs7033979	0.95[CEU][hapmap]
rs7036459	0.91[LWK][hapmap];0.81[MKK][hapmap];0.84[YRI][hapmap]
rs7037075	0.84[CEU][hapmap]
rs7037194	0.87[CEU][hapmap]
rs7043984	0.91[CEU][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs7046335	0.89[EUR][1000 genomes]
rs724102	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs747629	0.84[CEU][hapmap]
rs755209	0.94[AMR][1000 genomes];0.93[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];0.85[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7860786	0.87[CEU][hapmap]
rs7864575	0.95[CEU][hapmap];0.90[TSI][hapmap]
rs7864630	0.84[CEU][hapmap]
rs7865019	0.95[CEU][hapmap];0.90[TSI][hapmap]
rs7865118	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7868013	0.95[CEU][hapmap];0.83[TSI][hapmap]
rs7869521	1.00[CEU][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7869742	0.84[CEU][hapmap]
rs8067	0.84[CEU][hapmap]
rs927865	0.87[CEU][hapmap]
rs9299405	0.95[CEU][hapmap];0.90[TSI][hapmap]
rs968040	0.95[CEU][hapmap];0.90[TSI][hapmap]

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7020104	CENPP	cis	Esophagus Muscularis	GTEx
rs7020104	CENPP	cis	parietal	SCAN
rs7020104	ZNF484	cis	parietal	SCAN
rs7020104	ZNF484	cis	cerebellum	SCAN
rs7020104	NOL8	cis	cerebellum	SCAN
rs7020104	CENPP	cis	Muscle Skeletal	GTEx
rs7020104	CENPP	cis	cerebellum	SCAN

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	chr9:95392000-95419600	Strong transcription	Primary T cells from cord blood	blood
6	chr9:95392400-95420800	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr9:95393200-95421200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr9:95393200-95421600	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr9:95393600-95421000	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr9:95393800-95419200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr9:95393800-95421000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr9:95394000-95420800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr9:95394200-95418800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr9:95394200-95419200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr9:95395000-95416600	Strong transcription	GM12878-XiMat	blood
16	chr9:95396000-95420000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr9:95396800-95422400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr9:95397200-95417800	Strong transcription	Liver	Liver
19	chr9:95397400-95417000	Strong transcription	Skeletal Muscle Male	skeletal muscle
20	chr9:95398200-95420800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr9:95400600-95417600	Weak transcription	Psoas Muscle	Psoas
22	chr9:95401200-95421800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr9:95401200-95422000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:95401400-95417200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr9:95404200-95417200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr9:95408000-95420800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr9:95408400-95421200	Strong transcription	Brain Germinal Matrix	brain
28	chr9:95408600-95420800	Strong transcription	Fetal Brain Female	brain
29	chr9:95408800-95421000	Strong transcription	Thymus	Thymus
30	chr9:95408800-95426800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr9:95409600-95417400	Strong transcription	Fetal Muscle Trunk	muscle
32	chr9:95409600-95421200	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr9:95409800-95417200	Strong transcription	Fetal Muscle Leg	muscle
34	chr9:95409800-95420200	Strong transcription	Lung	lung
35	chr9:95409800-95431000	Weak transcription	Fetal Kidney	kidney
36	chr9:95410000-95418200	Strong transcription	Fetal Intestine Small	intestine
37	chr9:95410200-95420800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr9:95410400-95420800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr9:95410400-95420800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr9:95410800-95417400	Weak transcription	Hela-S3	cervix
41	chr9:95410800-95427000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr9:95411000-95431400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr9:95411400-95420200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr9:95411400-95421800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr9:95411600-95417400	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr9:95411600-95420800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr9:95411800-95416800	Weak transcription	Brain Angular Gyrus	brain
48	chr9:95411800-95419800	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr9:95411800-95426600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr9:95411800-95427400	Weak transcription	Pancreatic Islets	Pancreatic Islet

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