Variant report

Variant	rs11706203
Chromosome Location	chr3:48746239-48746240
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:48732590..48735474-chr3:48745317..48746995,2	K562	blood:
2	chr3:48738710..48740222-chr3:48745168..48747934,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000068745	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10865952	0.95[ASN][1000 genomes]
rs11557629	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11706983	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11708786	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715177	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715689	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11715713	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11715835	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11719291	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719457	0.80[AMR][1000 genomes]
rs12493578	0.95[ASN][1000 genomes]
rs12497850	0.95[ASN][1000 genomes]
rs12715429	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13063223	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13070798	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13076269	0.81[AMR][1000 genomes]
rs13086240	0.84[AMR][1000 genomes]
rs13090013	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13090839	0.80[AMR][1000 genomes]
rs13096357	0.81[AMR][1000 genomes]
rs13316551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13324119	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13324950	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13434258	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1352420	0.95[ASN][1000 genomes]
rs17080319	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286651	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2286652	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2302295	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28452701	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28567949	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28657585	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28793701	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34096717	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34153629	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34577723	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs35064573	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733086	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3821875	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4077495	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858798	0.95[ASN][1000 genomes]
rs4858828	0.95[ASN][1000 genomes]
rs4858831	0.95[ASN][1000 genomes]
rs56735597	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61137521	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6768448	0.82[EUR][1000 genomes]
rs6773261	0.81[AMR][1000 genomes]
rs6788650	0.95[ASN][1000 genomes]
rs68042649	0.82[EUR][1000 genomes]
rs7633840	0.86[ASN][1000 genomes]
rs9809222	0.82[EUR][1000 genomes]
rs9811027	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9811318	0.82[EUR][1000 genomes]
rs9812977	0.80[AMR][1000 genomes]
rs9821797	0.82[EUR][1000 genomes]
rs9834996	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836462	0.82[EUR][1000 genomes]
rs9841602	0.82[EUR][1000 genomes]
rs9848203	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9854034	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9873726	0.82[EUR][1000 genomes]
rs9877542	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9877685	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9882549	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv590247	chr3:48661985-48801929	Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11706203	WDR6	cis	Whole Blood	GTEx
rs11706203	WDR6	cis	Esophagus Mucosa	GTEx
rs11706203	WDR6	cis	Adipose Subcutaneous	GTEx
rs11706203	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs11706203	WDR6	cis	lung	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48724600-48746600	Strong transcription	Fetal Thymus	thymus
2	chr3:48724600-48749000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:48733000-48753400	Weak transcription	Aorta	Aorta
4	chr3:48734000-48746400	Weak transcription	Fetal Brain Male	brain
5	chr3:48734400-48746400	Weak transcription	Stomach Mucosa	stomach
6	chr3:48734400-48748800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:48737200-48746600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:48737400-48746400	Weak transcription	HSMMtube	muscle
9	chr3:48738200-48752400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr3:48739800-48750800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:48740000-48753600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr3:48740400-48746600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:48740600-48747400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr3:48741400-48750600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr3:48741600-48749600	Strong transcription	Primary B cells from cord blood	blood
16	chr3:48741600-48750600	Strong transcription	Fetal Muscle Trunk	muscle
17	chr3:48741600-48752400	Strong transcription	Fetal Intestine Large	intestine
18	chr3:48741800-48746400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:48741800-48749400	Strong transcription	Fetal Stomach	stomach
20	chr3:48741800-48751800	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr3:48741800-48752400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr3:48741800-48752600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr3:48742000-48746400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr3:48742000-48748800	Strong transcription	Thymus	Thymus
25	chr3:48742800-48750000	Strong transcription	Placenta	Placenta
26	chr3:48742800-48750800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr3:48743000-48749600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr3:48743000-48752400	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr3:48743000-48753000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr3:48743400-48746400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr3:48743400-48746400	Strong transcription	Duodenum Mucosa	Duodenum
32	chr3:48743600-48746600	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr3:48743600-48750600	Strong transcription	Hela-S3	cervix
34	chr3:48743600-48751200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr3:48743600-48751800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
36	chr3:48743600-48752000	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr3:48743800-48747800	Genic enhancers	Duodenum Smooth Muscle	Duodenum
38	chr3:48743800-48752800	Genic enhancers	Primary T cells fromperipheralblood	blood
39	chr3:48744600-48746800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr3:48744600-48747600	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr3:48744600-48747600	Enhancers	Right Atrium	heart
42	chr3:48744600-48749400	Strong transcription	Liver	Liver
43	chr3:48744600-48749600	Strong transcription	HUVEC	blood vessel
44	chr3:48744600-48751000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
45	chr3:48744600-48751200	Genic enhancers	Primary T cells from cord blood	blood
46	chr3:48744800-48746600	Strong transcription	Colon Smooth Muscle	Colon
47	chr3:48744800-48747000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr3:48744800-48750600	Genic enhancers	Brain Germinal Matrix	brain
49	chr3:48745000-48746800	Enhancers	Ovary	ovary
50	chr3:48745000-48747800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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