Variant report

Variant	rs11708786
Chromosome Location	chr3:48752654-48752655
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:48725593..48727125-chr3:48750747..48752784,2	MCF-7	breast:
2	chr3:48752504..48754633-chr3:49057932..49060797,2	K562	blood:
3	chr3:48732542..48735376-chr3:48750993..48752883,2	K562	blood:

Variant related genes	Relation type
ENSG00000207605	Chromatin interaction
ENSG00000178149	Chromatin interaction
ENSG00000068745	Chromatin interaction
ENSG00000178057	Chromatin interaction

Extended variants
information (count: 130 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:129)

rs_ID	r²[population]
rs1003649	0.83[GIH][hapmap]
rs10470687	0.83[GIH][hapmap]
rs1048940	0.84[CEU][hapmap]
rs10780033	1.00[CHD][hapmap]
rs10865952	0.95[ASN][1000 genomes]
rs11130176	1.00[CHD][hapmap]
rs11557629	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11706203	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11706983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11708022	0.84[AMR][1000 genomes]
rs11709092	0.80[AMR][1000 genomes]
rs11709246	0.84[AMR][1000 genomes]
rs11713694	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes]
rs11715177	1.00[AMR][1000 genomes];0.98[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	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11719291	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11920534	1.00[CHD][hapmap]
rs11928552	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs12107252	1.00[GIH][hapmap]
rs12107418	1.00[GIH][hapmap]
rs12493289	1.00[JPT][hapmap]
rs12493578	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12497850	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12715429	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13060933	0.83[GIH][hapmap]
rs13063223	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13063312	1.00[GIH][hapmap];0.81[TSI][hapmap]
rs13070798	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13073997	0.84[AMR][1000 genomes]
rs13074318	0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes]
rs13084000	0.84[AMR][1000 genomes]
rs13087930	0.84[AMR][1000 genomes]
rs13090013	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13094900	0.80[AMR][1000 genomes]
rs13316551	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13319651	0.83[GIH][hapmap]
rs13324119	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13324142	1.00[GIH][hapmap];0.81[TSI][hapmap]
rs13324950	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13434258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1352420	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17080289	1.00[GIH][hapmap]
rs17080319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2006871	0.83[GIH][hapmap]
rs2276850	1.00[GIH][hapmap];0.81[TSI][hapmap]
rs2276852	1.00[GIH][hapmap]
rs2286651	0.80[AMR][1000 genomes]
rs2286652	1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes]
rs2302295	0.87[AMR][1000 genomes]
rs2310996	1.00[GIH][hapmap]
rs28452701	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2854394	0.83[GIH][hapmap]
rs28567949	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28657585	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28793701	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34037363	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.85[TSI][hapmap]
rs34096717	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34153629	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34477108	0.84[AMR][1000 genomes]
rs34509487	0.84[AMR][1000 genomes]
rs34577723	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs35064573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733086	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3806694	1.00[JPT][hapmap]
rs3821875	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3821876	1.00[GIH][hapmap];0.81[TSI][hapmap]
rs3969942	0.83[GIH][hapmap]
rs4077495	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858798	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4858828	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4858831	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4974079	1.00[CHD][hapmap]
rs4974085	1.00[CHD][hapmap]
rs4974087	1.00[CHD][hapmap]
rs56735597	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61137521	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6442130	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs67060340	0.80[AMR][1000 genomes]
rs67332931	0.84[AMR][1000 genomes]
rs6781283	0.83[GIH][hapmap]
rs6788650	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6791542	1.00[CHD][hapmap]
rs6792156	1.00[GIH][hapmap]
rs6792525	0.83[GIH][hapmap]
rs6806059	0.83[GIH][hapmap]
rs71324924	0.84[AMR][1000 genomes]
rs740787	1.00[GIH][hapmap]
rs7430501	1.00[CHD][hapmap]
rs7431710	1.00[CHD][hapmap]
rs7431857	1.00[CHD][hapmap]
rs7623023	1.00[CHD][hapmap]
rs7627404	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7631574	1.00[GIH][hapmap]
rs7633840	0.86[ASN][1000 genomes]
rs7647813	1.00[CHD][hapmap]
rs7649458	1.00[CHD][hapmap]
rs9311430	1.00[CHD][hapmap]
rs9311433	1.00[CHD][hapmap]
rs9311434	1.00[CHD][hapmap]
rs9682444	0.87[CHD][hapmap]
rs9755490	0.87[CHD][hapmap]
rs9810549	0.83[GIH][hapmap]
rs9810991	0.83[GIH][hapmap]
rs9811027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9811318	1.00[GIH][hapmap]
rs9812200	1.00[GIH][hapmap]
rs9830581	1.00[GIH][hapmap]
rs9834996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9835307	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs9836462	1.00[GIH][hapmap]
rs9837687	0.83[GIH][hapmap]
rs9841602	1.00[GIH][hapmap]
rs9843316	1.00[GIH][hapmap]
rs9848203	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9850102	0.83[GIH][hapmap]
rs9854034	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9868809	0.83[GIH][hapmap]
rs9869698	0.83[GIH][hapmap]
rs9871180	1.00[GIH][hapmap]
rs9873726	1.00[JPT][hapmap]
rs9876848	1.00[CHD][hapmap]
rs9877542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9877685	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9878950	0.83[GIH][hapmap]
rs9881877	1.00[GIH][hapmap]
rs9882549	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9882962	0.83[GIH][hapmap]

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:17)

SNP	Gene	Cis/trans	Tissue	Source
rs11708786	WDR6	cis	Adipose Subcutaneous	GTEx
rs11708786	USP4	cis	multi-tissue	Pritchard
rs11708786	WDR6	cis	lymphoblastoid	seeQTL
rs11708786	C3orf62	cis	parietal	SCAN
rs11708786	NCKIPSD	cis	parietal	SCAN
rs11708786	WDR6	cis	multi-tissue	Pritchard
rs11708786	WDR6	cis	Whole Blood	GTEx
rs11708786	WDR6	cis	lung	GTEx
rs11708786	WDR6	cis	Esophagus Mucosa	GTEx
rs11708786	WDR6	cis	cerebellum	SCAN
rs11708786	RNF123	cis	parietal	SCAN
rs11708786	C3orf62	cis	cerebellum	SCAN
rs11708786	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs11708786	CSPG5	cis	parietal	SCAN
rs11708786	WDR6	cis	parietal	SCAN
rs11708786	LRRC2	cis	cerebellum	SCAN
rs11708786	ALAS1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48733000-48753400	Weak transcription	Aorta	Aorta
2	chr3:48740000-48753600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:48743000-48753000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:48743800-48752800	Genic enhancers	Primary T cells fromperipheralblood	blood
5	chr3:48745600-48752800	Weak transcription	Small Intestine	intestine
6	chr3:48745800-48753400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr3:48748800-48753000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr3:48749000-48752800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr3:48749400-48753400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:48749800-48753000	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr3:48750000-48752800	Genic enhancers	Primary B cells from peripheral blood	blood
12	chr3:48750000-48753200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:48750000-48753200	Genic enhancers	Placenta	Placenta
14	chr3:48750200-48752800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr3:48750600-48752800	Enhancers	Fetal Heart	heart
16	chr3:48750600-48752800	Genic enhancers	HepG2	liver
17	chr3:48750600-48753000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr3:48751000-48752800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:48751000-48752800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr3:48751000-48752800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr3:48751000-48752800	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr3:48751000-48752800	Enhancers	Duodenum Smooth Muscle	Duodenum
23	chr3:48751000-48752800	Genic enhancers	Hela-S3	cervix
24	chr3:48751000-48753400	Weak transcription	Ovary	ovary
25	chr3:48751000-48753800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr3:48751000-48754000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:48751000-48754000	Weak transcription	Gastric	stomach
28	chr3:48751200-48755000	Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr3:48751800-48752800	Genic enhancers	Primary monocytes fromperipheralblood	blood
30	chr3:48751800-48753000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr3:48751800-48753000	Enhancers	Spleen	Spleen
32	chr3:48751800-48753200	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr3:48752000-48752800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr3:48752000-48753000	Enhancers	Lung	lung
35	chr3:48752000-48753000	Genic enhancers	Pancreas	Pancrea
36	chr3:48752000-48753200	Genic enhancers	Liver	Liver
37	chr3:48752000-48754000	Weak transcription	Esophagus	oesophagus
38	chr3:48752200-48752800	Genic enhancers	Cortex derived primary cultured neurospheres	brain
39	chr3:48752200-48753000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr3:48752200-48753000	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum
41	chr3:48752200-48753000	Genic enhancers	Fetal Muscle Leg	muscle
42	chr3:48752200-48753000	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr3:48752200-48753200	Flanking Active TSS	HMEC	breast
44	chr3:48752400-48752800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr3:48752400-48752800	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr3:48752400-48752800	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:48752400-48752800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr3:48752400-48752800	Enhancers	Colon Smooth Muscle	Colon
49	chr3:48752400-48752800	Genic enhancers	Fetal Intestine Large	intestine
50	chr3:48752400-48752800	Enhancers	Pancreatic Islets	Pancreatic Islet

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