Variant report

Variant	rs12236013
Chromosome Location	chr9:95416398-95416399
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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:

Variant related genes	Relation type
ENSG00000185963	Chromatin interaction
ENSG00000127080	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10491806	0.89[AMR][1000 genomes]
rs10820997	0.83[AMR][1000 genomes]
rs10820998	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10821001	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10821003	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10821004	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10821005	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10821011	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10821014	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10992367	0.90[AMR][1000 genomes]
rs10992380	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10992382	0.81[AMR][1000 genomes]
rs10992384	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10992390	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10992392	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992394	0.93[ASN][1000 genomes]
rs10992396	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10992404	0.88[ASN][1000 genomes]
rs10992406	0.88[ASN][1000 genomes]
rs10992407	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10992408	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10992409	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10992412	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10992414	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10992416	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10992417	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10992418	0.82[AMR][1000 genomes]
rs10992420	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10992422	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10992423	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10992437	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10992448	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10992453	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10992460	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10992461	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1117670	0.81[AMR][1000 genomes]
rs11533010	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11535540	0.82[AMR][1000 genomes]
rs12236754	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12237216	0.87[ASN][1000 genomes]
rs12238691	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12684076	0.84[EUR][1000 genomes]
rs12684587	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12685358	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12686780	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12686781	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1323523	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1326775	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1575460	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17366488	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1853468	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2038685	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2088054	0.88[AMR][1000 genomes]
rs2088055	0.84[AMR][1000 genomes]
rs2131919	0.90[AMR][1000 genomes]
rs2146848	0.82[EUR][1000 genomes]
rs2148537	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2172716	0.90[AMR][1000 genomes]
rs2181584	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2277166	0.82[ASN][1000 genomes]
rs2277169	0.82[EUR][1000 genomes]
rs3739605	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56311406	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs57737182	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58952648	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60498616	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6479426	0.81[AMR][1000 genomes]
rs67601697	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7031163	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs753804	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs754600	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7853617	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7856147	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7857105	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7857502	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7860628	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7862106	0.82[AMR][1000 genomes]
rs7863741	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7863882	0.81[AMR][1000 genomes]
rs7863890	0.81[ASN][1000 genomes]
rs7869603	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7875050	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs879812	0.81[ASN][1000 genomes]
rs912261	0.88[ASN][1000 genomes]
rs912264	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs971984	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12236013	CENPP	cis	multi-tissue	Pritchard

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	chr9:95408000-95416400	Strong transcription	Primary B cells from peripheral blood	blood
27	chr9:95408000-95420800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr9:95408400-95421200	Strong transcription	Brain Germinal Matrix	brain
29	chr9:95408600-95420800	Strong transcription	Fetal Brain Female	brain
30	chr9:95408800-95421000	Strong transcription	Thymus	Thymus
31	chr9:95408800-95426800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr9:95409600-95417400	Strong transcription	Fetal Muscle Trunk	muscle
33	chr9:95409600-95421200	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr9:95409800-95417200	Strong transcription	Fetal Muscle Leg	muscle
35	chr9:95409800-95420200	Strong transcription	Lung	lung
36	chr9:95409800-95431000	Weak transcription	Fetal Kidney	kidney
37	chr9:95410000-95416400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr9:95410000-95418200	Strong transcription	Fetal Intestine Small	intestine
39	chr9:95410200-95420800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr9:95410400-95420800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr9:95410400-95420800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr9:95410800-95417400	Weak transcription	Hela-S3	cervix
43	chr9:95410800-95427000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr9:95411000-95431400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr9:95411400-95420200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr9:95411400-95421800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr9:95411600-95417400	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr9:95411600-95420800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr9:95411800-95416800	Weak transcription	Brain Angular Gyrus	brain
50	chr9:95411800-95419800	Weak transcription	H1 Cell Line	embryonic stem cell

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