Variant report

Variant	rs7647813
Chromosome Location	chr3:48833348-48833349
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 37 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10780033	0.89[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap]
rs11130176	0.89[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs1134591	0.89[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap]
rs11706983	1.00[CHD][hapmap]
rs11708786	1.00[CHD][hapmap]
rs11713694	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11719291	1.00[CHD][hapmap]
rs11920534	0.89[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap]
rs11924597	1.00[CEU][hapmap]
rs11928552	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap]
rs12493289	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12493578	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.86[TSI][hapmap]
rs12497850	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap]
rs13086240	1.00[JPT][hapmap]
rs13087930	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs13092715	0.89[ASW][hapmap];0.82[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs13315711	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs13434258	1.00[CHD][hapmap]
rs1352420	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap]
rs34037363	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs35064573	1.00[CHD][hapmap]
rs3774628	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap]
rs4858798	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap]
rs4858828	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap]
rs4858831	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap]
rs4974078	0.87[CHD][hapmap]
rs4974079	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap]
rs4974080	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap]
rs4974082	0.89[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap]
rs4974085	0.89[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap]
rs4974087	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap]
rs6442130	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap]
rs6446196	1.00[CEU][hapmap];0.81[GIH][hapmap];0.81[LWK][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap]
rs6446252	1.00[CEU][hapmap];0.86[YRI][hapmap]
rs6446253	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6768433	1.00[CEU][hapmap]
rs6788650	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap]
rs6791542	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap]
rs7430198	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap]
rs7430501	0.89[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap]
rs7431710	0.89[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap]
rs7431857	0.89[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap]
rs7616815	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap]
rs7621015	0.89[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap]
rs7623023	0.89[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap]
rs7627404	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap]
rs7628719	0.89[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap]
rs7643368	0.89[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap]
rs7649458	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs9311430	0.89[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs9311432	1.00[CEU][hapmap]
rs9311433	0.89[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs9311434	0.89[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap]
rs9637481	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs9682444	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap]
rs9755490	1.00[CEU][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap]
rs9835307	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap]
rs9850134	0.89[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap]
rs9873726	1.00[CHB][hapmap]
rs9876848	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap]
rs9882549	1.00[CHD][hapmap]
rs9884022	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487342	chr3:48823957-48960475	Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	esv3487343	chr3:48823963-48960381	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:37)

SNP	Gene	Cis/trans	Tissue	Source
rs7647813	WDR6	cis	cerebellum	SCAN
rs7647813	CCDC71	cis	cerebellum	SCAN
rs7647813	WDR6	cis	Artery Tibial	GTEx
rs7647813	WDR6	cis	Heart Left Ventricle	GTEx
rs7647813	AMT	cis	cerebellum	SCAN
rs7647813	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs7647813	ARIH2	Cis_1M	lymphoblastoid	RTeQTL
rs7647813	AMT	cis	Whole Blood	GTEx
rs7647813	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs7647813	TLR9	cis	parietal	SCAN
rs7647813	PHF7	cis	parietal	SCAN
rs7647813	AMT	cis	Artery Aorta	GTEx
rs7647813	WDR6	cis	Whole Blood	GTEx
rs7647813	NCKIPSD	cis	cerebellum	SCAN
rs7647813	NCKIPSD	cis	Whole Blood	GTEx
rs7647813	CCDC36	cis	Artery Tibial	GTEx
rs7647813	NCKIPSD	cis	Nerve Tibial	GTEx
rs7647813	P4HTM	cis	cerebellum	SCAN
rs7647813	P4HTM	cis	parietal	SCAN
rs7647813	NCKIPSD	cis	parietal	SCAN
rs7647813	AMT	cis	parietal	SCAN
rs7647813	ARIH2	cis	Thyroid	GTEx
rs7647813	WDR6	cis	Adipose Subcutaneous	GTEx
rs7647813	WDR6	cis	Esophagus Muscularis	GTEx
rs7647813	NICN1-AS1	cis	Thyroid	GTEx
rs7647813	NCKIPSD	cis	Muscle Skeletal	GTEx
rs7647813	AMT	cis	Thyroid	GTEx
rs7647813	WDR6	cis	lymphoblastoid	seeQTL
rs7647813	WDR6	cis	Esophagus Mucosa	GTEx
rs7647813	NICN1	cis	Thyroid	GTEx
rs7647813	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs7647813	DALRD3	cis	parietal	SCAN
rs7647813	WDR6	cis	Muscle Skeletal	GTEx
rs7647813	DALRD3	cis	cerebellum	SCAN
rs7647813	WDR6	cis	Nerve Tibial	GTEx
rs7647813	WDR6	cis	lung	GTEx
rs7647813	WDR6	cis	parietal	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48778200-48836600	Weak transcription	A549	lung
2	chr3:48789400-48844000	Weak transcription	Fetal Lung	lung
3	chr3:48795200-48833600	Weak transcription	Psoas Muscle	Psoas
4	chr3:48809000-48849400	Weak transcription	GM12878-XiMat	blood
5	chr3:48810000-48882800	Weak transcription	Fetal Brain Female	brain
6	chr3:48810400-48848600	Weak transcription	Brain Anterior Caudate	brain
7	chr3:48810600-48835000	Weak transcription	HUVEC	blood vessel
8	chr3:48810600-48842600	Weak transcription	Pancreas	Pancrea
9	chr3:48810800-48836600	Weak transcription	Hela-S3	cervix
10	chr3:48820400-48868200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:48820600-48836200	Weak transcription	Fetal Kidney	kidney
12	chr3:48820600-48840200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:48820600-48882800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:48820800-48843200	Weak transcription	Right Ventricle	heart
15	chr3:48820800-48847200	Weak transcription	NHDF-Ad	bronchial
16	chr3:48821000-48833400	Weak transcription	HSMM	muscle
17	chr3:48821000-48840600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:48821000-48849000	Weak transcription	NHLF	lung
19	chr3:48821000-48858000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr3:48821000-48858200	Weak transcription	Gastric	stomach
21	chr3:48822200-48843600	Weak transcription	Fetal Intestine Large	intestine
22	chr3:48822200-48855800	Weak transcription	Lung	lung
23	chr3:48822400-48833600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr3:48822400-48833800	Weak transcription	Brain Substantia Nigra	brain
25	chr3:48822400-48848600	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr3:48822400-48857800	Weak transcription	NHEK	skin
27	chr3:48822400-48858200	Weak transcription	HSMMtube	muscle
28	chr3:48822600-48833400	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr3:48824000-48842800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr3:48825600-48836400	Weak transcription	Liver	Liver
31	chr3:48825800-48837800	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr3:48826400-48868400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr3:48826600-48833600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr3:48826600-48842600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr3:48826800-48833800	Weak transcription	K562	blood
36	chr3:48826800-48841000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr3:48826800-48842000	Weak transcription	Aorta	Aorta
38	chr3:48826800-48842400	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr3:48826800-48847200	Weak transcription	Primary T cells from cord blood	blood
40	chr3:48826800-48847200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr3:48826800-48847200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr3:48826800-48847200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:48826800-48847600	Weak transcription	Brain Germinal Matrix	brain
44	chr3:48826800-48848800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr3:48826800-48858200	Weak transcription	Brain Angular Gyrus	brain
46	chr3:48826800-48869600	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr3:48826800-48882800	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr3:48827000-48847200	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr3:48827000-48847200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr3:48827000-48848800	Weak transcription	Brain Hippocampus Middle	brain

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