Variant report

Variant	rs17650792
Chromosome Location	chr3:49390250-49390251
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	chr3:49376884..49378442-chr3:49388681..49390711,2	MCF-7	breast:
2	chr3:49388313..49390760-chr3:49397473..49400161,2	K562	blood:

Variant related genes	Relation type
ENSG00000114316	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1050088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs1050450	0.94[ASN][1000 genomes]
rs10640	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs10865955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11130192	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11130193	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11130194	0.88[EUR][1000 genomes]
rs11130196	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11130199	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.83[EUR][1000 genomes]
rs11130202	1.00[CEU][hapmap]
rs11706370	1.00[JPT][hapmap]
rs11711485	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs11711536	0.94[ASN][1000 genomes]
rs11715915	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs11716974	0.82[ASN][1000 genomes]
rs11720264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs11922013	1.00[JPT][hapmap]
rs12489092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs13078949	0.85[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs13086611	0.94[ASN][1000 genomes]
rs13087851	0.94[ASN][1000 genomes]
rs13090388	0.94[ASN][1000 genomes]
rs13096760	0.90[EUR][1000 genomes]
rs1464566	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1464567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1464568	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1568661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.83[EUR][1000 genomes]
rs1568662	0.82[EUR][1000 genomes]
rs17080528	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17595772	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1800668	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1801143	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs1987628	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2117939	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2878298	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34588335	0.94[ASN][1000 genomes]
rs34937635	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35169793	0.94[ASN][1000 genomes]
rs35701831	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3811699	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3870338	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap]
rs3877784	0.83[EUR][1000 genomes]
rs3924462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.83[EUR][1000 genomes]
rs4459909	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4563439	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4625	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs4855839	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs4855842	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4855843	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4855859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.83[EUR][1000 genomes]
rs4855861	0.81[EUR][1000 genomes]
rs4855864	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.83[EUR][1000 genomes]
rs4855866	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4855873	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4855877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4955412	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955438	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55957735	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59152804	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62259939	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62259942	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6446264	0.94[ASN][1000 genomes]
rs6446272	0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs6446274	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs67485053	0.88[ASN][1000 genomes]
rs6766131	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs6773518	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6779524	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs6784820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6792911	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6793308	0.94[ASN][1000 genomes]
rs6797765	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809216	0.94[ASN][1000 genomes]
rs6997	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs7371895	0.81[EUR][1000 genomes]
rs7373849	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7621003	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7622302	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs7623659	0.94[ASN][1000 genomes]
rs7631908	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7633271	1.00[JPT][hapmap]
rs7637999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.83[EUR][1000 genomes]
rs7643586	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7643845	0.82[EUR][1000 genomes]
rs7645445	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7646366	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs7648841	0.94[ASN][1000 genomes]
rs885592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9814873	0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs9827021	1.00[JPT][hapmap]
rs9841110	1.00[JPT][hapmap]
rs9853683	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]

mRNA abundance (count:21)

SNP	Gene	Cis/trans	Tissue	Source
rs17650792	GNL3	cis	cerebellum	SCAN
rs17650792	WDR6	cis	cerebellum	SCAN
rs17650792	QRICH1	cis	parietal	SCAN
rs17650792	WDR6	cis	Adipose Subcutaneous	GTEx
rs17650792	WDR6	cis	Muscle Skeletal	GTEx
rs17650792	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs17650792	AMT	cis	cerebellum	SCAN
rs17650792	WDR6	cis	Nerve Tibial	GTEx
rs17650792	P4HTM	cis	cerebellum	SCAN
rs17650792	WDR6	cis	Whole Blood	GTEx
rs17650792	WDR6	cis	parietal	SCAN
rs17650792	WDR6	cis	lung	GTEx
rs17650792	IP6K2	cis	cerebellum	SCAN
rs17650792	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs17650792	CCDC71	cis	cerebellum	SCAN
rs17650792	NCKIPSD	cis	cerebellum	SCAN
rs17650792	WDR6	cis	Artery Tibial	GTEx
rs17650792	DALRD3	cis	cerebellum	SCAN
rs17650792	P4HTM	cis	parietal	SCAN
rs17650792	AMT	cis	Thyroid	GTEx
rs17650792	TLR9	cis	parietal	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49378600-49392000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr3:49379000-49392000	Weak transcription	Left Ventricle	heart
3	chr3:49379800-49392800	Weak transcription	Thymus	Thymus
4	chr3:49381600-49393000	Weak transcription	Right Atrium	heart
5	chr3:49383000-49393600	Weak transcription	Primary T cells from cord blood	blood
6	chr3:49383200-49391800	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr3:49383200-49392400	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr3:49383400-49391400	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr3:49384600-49392000	Weak transcription	Fetal Muscle Leg	muscle
10	chr3:49384600-49392400	Weak transcription	Fetal Muscle Trunk	muscle
11	chr3:49384800-49391800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr3:49386400-49390800	Enhancers	Primary hematopoietic stem cells	blood
13	chr3:49386400-49390800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr3:49386400-49390800	Enhancers	Adipose Nuclei	Adipose
15	chr3:49386400-49390800	Enhancers	K562	blood
16	chr3:49386800-49390400	Enhancers	Placenta	Placenta
17	chr3:49387000-49393000	Weak transcription	Aorta	Aorta
18	chr3:49387200-49391400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr3:49387200-49392800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr3:49387400-49392800	Weak transcription	Stomach Smooth Muscle	stomach
21	chr3:49387400-49393000	Weak transcription	Right Ventricle	heart
22	chr3:49387400-49393800	Weak transcription	Gastric	stomach
23	chr3:49387600-49390800	Enhancers	Primary B cells from cord blood	blood
24	chr3:49387800-49393000	Weak transcription	Dnd41	blood
25	chr3:49388000-49390800	Enhancers	Esophagus	oesophagus
26	chr3:49388000-49391400	Enhancers	GM12878-XiMat	blood
27	chr3:49388200-49390400	Enhancers	HMEC	breast
28	chr3:49388200-49390600	Enhancers	HSMM	muscle
29	chr3:49388200-49390800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr3:49388200-49390800	Enhancers	Primary B cells from peripheral blood	blood
31	chr3:49388200-49390800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr3:49388200-49390800	Enhancers	NHLF	lung
33	chr3:49388200-49390800	Enhancers	Osteobl	bone
34	chr3:49388400-49390600	Enhancers	NHEK	skin
35	chr3:49388400-49390800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:49388400-49392600	Weak transcription	Lung	lung
37	chr3:49388400-49393000	Weak transcription	Colonic Mucosa	Colon
38	chr3:49388600-49390800	Enhancers	HUVEC	blood vessel
39	chr3:49388800-49390400	Enhancers	Stomach Mucosa	stomach
40	chr3:49388800-49390600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr3:49388800-49390600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:49388800-49390600	Enhancers	Fetal Thymus	thymus
43	chr3:49388800-49390600	Enhancers	HSMMtube	muscle
44	chr3:49388800-49390800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
45	chr3:49388800-49393600	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr3:49389000-49390400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr3:49389000-49390400	Enhancers	NH-A	brain
48	chr3:49389000-49392800	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr3:49389200-49390800	Enhancers	Muscle Satellite Cultured Cells	--
50	chr3:49389200-49394600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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