Variant report

Variant	rs9985404
Chromosome Location	chr3:17095401-17095402
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10865746	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11128815	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11717329	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11926952	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12233492	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12487288	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12497667	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12497953	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13058764	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13059347	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13071645	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13080108	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13080782	0.83[EUR][1000 genomes]
rs13317381	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1441035	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17272796	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1806555	0.84[EUR][1000 genomes]
rs1806556	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1837697	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35319117	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3906814	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3924971	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4234539	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4295151	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4353792	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4423750	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4461404	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4472039	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4535211	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4561816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4596131	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4602367	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4685404	0.89[ASN][1000 genomes]
rs4685408	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4685409	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4685415	0.86[AMR][1000 genomes]
rs4685418	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4685420	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4685421	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55748719	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6762816	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6776032	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6780191	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6781611	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6797029	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6805534	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6807144	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6809087	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7610811	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7611127	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7612044	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7617672	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7629171	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7645335	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7653027	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9810017	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9830460	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9841259	0.85[ASN][1000 genomes]
rs9844888	0.88[ASN][1000 genomes]
rs9854760	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9862613	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9880307	0.83[ASN][1000 genomes]
rs9881521	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9985404	PLCL2	cis	Whole Blood	GTEx

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:17081200-17111400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:17082600-17097000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:17083000-17096600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:17083000-17097200	Weak transcription	NH-A	brain
5	chr3:17083000-17109600	Weak transcription	Fetal Intestine Large	intestine
6	chr3:17083200-17111600	Weak transcription	Stomach Mucosa	stomach
7	chr3:17085000-17095800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr3:17085800-17112200	Weak transcription	Gastric	stomach
9	chr3:17086000-17096000	Weak transcription	Right Ventricle	heart
10	chr3:17086000-17096400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr3:17089400-17109000	Weak transcription	Dnd41	blood
12	chr3:17089400-17135000	Weak transcription	Pancreas	Pancrea
13	chr3:17089600-17097000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:17089600-17111000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr3:17089800-17110400	Weak transcription	Fetal Thymus	thymus
16	chr3:17089800-17112200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr3:17089800-17116000	Weak transcription	Thymus	Thymus
18	chr3:17090000-17095800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:17090400-17096000	Weak transcription	Fetal Heart	heart
20	chr3:17090400-17096400	Weak transcription	Osteobl	bone
21	chr3:17090400-17097000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr3:17090400-17097000	Weak transcription	Left Ventricle	heart
23	chr3:17090400-17110400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr3:17090600-17096800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:17090600-17110400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr3:17091400-17095800	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr3:17091600-17103800	Strong transcription	Primary T cells from cord blood	blood
28	chr3:17092000-17109200	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr3:17092200-17095600	Strong transcription	Placenta	Placenta
30	chr3:17092200-17096000	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr3:17092200-17096800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:17092200-17109000	Weak transcription	Liver	Liver
33	chr3:17094400-17098600	Weak transcription	Primary B cells from peripheral blood	blood
34	chr3:17094600-17095600	ZNF genes & repeats	GM12878-XiMat	blood
35	chr3:17094600-17095800	ZNF genes & repeats	Brain Germinal Matrix	brain
36	chr3:17094600-17097400	Enhancers	Psoas Muscle	Psoas
37	chr3:17094800-17095600	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
38	chr3:17094800-17095800	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr3:17094800-17101400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr3:17094800-17112200	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr3:17095000-17095600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
42	chr3:17095000-17112000	Weak transcription	Right Atrium	heart
43	chr3:17095200-17098800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr3:17095200-17101800	Strong transcription	Primary B cells from cord blood	blood
45	chr3:17095200-17112200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr3:17095400-17096400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr3:17095400-17096400	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr3:17095400-17096400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr3:17095400-17097000	Weak transcription	Fetal Stomach	stomach
50	chr3:17095400-17099000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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