Variant report

Variant	rs12497667
Chromosome Location	chr3:17080974-17080975
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10865746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11128815	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11717329	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11926952	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12233492	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12487288	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12497953	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13058764	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13059347	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13071645	0.89[CEU][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13080108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13080782	0.83[EUR][1000 genomes]
rs13317381	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1441035	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17272796	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1806555	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs1806556	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1837697	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2014490	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs35319117	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3906814	0.88[CEU][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3924971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4234539	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4295151	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4334629	0.96[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap]
rs4353792	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4423750	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4461404	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4472039	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4535211	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4561816	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4596131	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4602367	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4618210	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs4684308	0.82[JPT][hapmap]
rs4685404	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4685405	0.86[JPT][hapmap]
rs4685408	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4685409	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4685415	0.86[AMR][1000 genomes]
rs4685418	0.88[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4685420	1.00[CEU][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4685421	1.00[CEU][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4685422	0.91[YRI][hapmap]
rs4685426	0.91[JPT][hapmap]
rs4685427	0.86[JPT][hapmap]
rs55748719	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6442660	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs6762816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6776032	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6780191	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6781611	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6797029	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6805534	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6807144	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6809087	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7610811	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7611127	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7612044	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7617672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7629171	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7645335	0.89[CEU][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7653027	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9810017	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9824172	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs9830460	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9841259	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs9844888	0.82[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs9854760	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9862613	0.96[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9879150	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs9880307	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9881521	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9883633	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs9985404	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12497667	PLCL2	cis	Whole Blood	GTEx

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:17053800-17086800	Weak transcription	Fetal Stomach	stomach
2	chr3:17055400-17088800	Weak transcription	Thymus	Thymus
3	chr3:17055800-17087800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:17058600-17082400	Weak transcription	Fetal Intestine Large	intestine
5	chr3:17060000-17082200	Weak transcription	Fetal Intestine Small	intestine
6	chr3:17060000-17088600	Weak transcription	Pancreas	Pancrea
7	chr3:17060200-17081000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr3:17065600-17081200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:17069400-17085600	Weak transcription	Aorta	Aorta
10	chr3:17070000-17093600	Weak transcription	Fetal Lung	lung
11	chr3:17072800-17085600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr3:17073000-17088800	Weak transcription	Right Atrium	heart
13	chr3:17073000-17093000	Weak transcription	Spleen	Spleen
14	chr3:17073200-17085200	Weak transcription	Placenta	Placenta
15	chr3:17073200-17085400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr3:17074000-17084400	Weak transcription	Liver	Liver
17	chr3:17075800-17081000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr3:17076400-17085600	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr3:17076600-17086800	Weak transcription	Dnd41	blood
20	chr3:17076800-17085200	Weak transcription	Primary B cells from peripheral blood	blood
21	chr3:17077000-17082000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr3:17077000-17086800	Weak transcription	Fetal Thymus	thymus
23	chr3:17077200-17083800	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr3:17077400-17084200	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr3:17077400-17085600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr3:17077400-17094600	Weak transcription	Psoas Muscle	Psoas
27	chr3:17077800-17084000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr3:17077800-17086800	Weak transcription	Ovary	ovary
29	chr3:17079000-17081600	Weak transcription	Primary T cells from cord blood	blood
30	chr3:17079600-17082000	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr3:17079600-17083200	Enhancers	Stomach Mucosa	stomach
32	chr3:17079800-17081400	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr3:17079800-17082200	Enhancers	Small Intestine	intestine
34	chr3:17079800-17082600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr3:17079800-17083000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr3:17079800-17083000	Enhancers	HUVEC	blood vessel
37	chr3:17079800-17090000	Strong transcription	Primary B cells from cord blood	blood
38	chr3:17080200-17081400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr3:17080200-17081400	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr3:17080200-17081600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr3:17080200-17082200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr3:17080200-17082400	Enhancers	Pancreatic Islets	Pancreatic Islet
43	chr3:17080200-17082600	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr3:17080200-17082800	Enhancers	HMEC	breast
45	chr3:17080200-17083000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:17080200-17083000	Enhancers	NHEK	skin
47	chr3:17080200-17083200	Enhancers	Hela-S3	cervix
48	chr3:17080400-17081000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr3:17080400-17081000	Enhancers	Lung	lung
50	chr3:17080400-17081000	Flanking Active TSS	A549	lung

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