Variant report

Variant	rs6947339
Chromosome Location	chr7:65888470-65888471
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 88 )
Associated
traits (count: 32 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1000464	1.00[CEU][hapmap];0.89[YRI][hapmap]
rs1002053	0.84[CEU][hapmap]
rs10107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs10215948	0.89[CEU][hapmap];0.85[TSI][hapmap]
rs10224872	1.00[CEU][hapmap];0.89[YRI][hapmap]
rs10228885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs10250544	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.98[MKK][hapmap];0.84[TSI][hapmap];0.94[YRI][hapmap]
rs10257427	0.88[CEU][hapmap]
rs10260426	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap]
rs10261398	1.00[CEU][hapmap];0.98[GIH][hapmap];0.86[LWK][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap]
rs10267430	0.88[CEU][hapmap]
rs10278014	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap]
rs10281499	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs10282433	1.00[CEU][hapmap];0.93[GIH][hapmap];0.86[LWK][hapmap];0.83[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap]
rs10447522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11760844	1.00[CEU][hapmap];0.89[YRI][hapmap]
rs11765965	0.82[CEU][hapmap]
rs11769079	0.93[YRI][hapmap]
rs11984115	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap]
rs12532998	0.89[CEU][hapmap];0.85[TSI][hapmap]
rs12537823	1.00[CEU][hapmap];0.98[GIH][hapmap];0.85[LWK][hapmap];0.82[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap]
rs12673450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs12698520	0.88[CEU][hapmap]
rs13536	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap]
rs1547529	0.82[YRI][hapmap]
rs1695820	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs17138149	0.82[YRI][hapmap]
rs1875057	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap]
rs1909508	0.82[YRI][hapmap]
rs1968225	0.89[CEU][hapmap]
rs2036264	0.89[CEU][hapmap];0.87[GIH][hapmap];0.87[TSI][hapmap];0.89[YRI][hapmap]
rs2077593	0.89[CEU][hapmap]
rs2088653	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap]
rs2088655	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs2173570	0.89[CEU][hapmap];0.89[YRI][hapmap]
rs2901152	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap]
rs3735148	0.89[CEU][hapmap];0.83[TSI][hapmap]
rs4149461	1.00[CEU][hapmap];0.98[GIH][hapmap];0.86[LWK][hapmap];0.83[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap]
rs4236208	1.00[CEU][hapmap];0.98[GIH][hapmap];0.86[LWK][hapmap];0.87[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap]
rs4718330	1.00[CEU][hapmap];0.93[GIH][hapmap];0.86[LWK][hapmap];0.83[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap]
rs6460282	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap]
rs6460292	0.89[CEU][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap]
rs6460293	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap]
rs6460296	0.89[CEU][hapmap]
rs6460302	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs6460304	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs6460307	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap]
rs6945019	0.89[CEU][hapmap]
rs6945032	0.89[CEU][hapmap]
rs6945843	0.92[CEU][hapmap];0.83[TSI][hapmap]
rs6950137	1.00[CEU][hapmap];0.94[YRI][hapmap]
rs6951503	0.96[CEU][hapmap]
rs6955837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs6956179	0.89[CEU][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap]
rs6959268	1.00[CEU][hapmap];0.98[GIH][hapmap];0.86[LWK][hapmap];0.83[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap]
rs6960446	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap]
rs6962717	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs6971509	0.89[CEU][hapmap];0.83[GIH][hapmap];0.89[TSI][hapmap];0.89[YRI][hapmap]
rs6974614	1.00[CEU][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap]
rs6976714	0.96[LWK][hapmap];0.94[YRI][hapmap]
rs709595	0.89[CEU][hapmap]
rs7782704	1.00[CEU][hapmap];0.89[YRI][hapmap]
rs7783613	0.89[CEU][hapmap];0.87[GIH][hapmap];0.87[TSI][hapmap];0.89[YRI][hapmap]
rs7783779	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap]
rs7783889	0.82[YRI][hapmap]
rs778697	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs778702	1.00[CEU][hapmap]
rs778706	0.89[CEU][hapmap]
rs778711	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs778720	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs778722	0.92[CEU][hapmap]
rs778734	1.00[CEU][hapmap];0.89[YRI][hapmap]
rs778736	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs7789768	0.89[CEU][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap]
rs7794930	0.89[CEU][hapmap];0.87[GIH][hapmap];0.87[TSI][hapmap];0.89[YRI][hapmap]
rs7798630	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.94[YRI][hapmap]
rs801195	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap]
rs801204	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs937495	0.89[CEU][hapmap];0.87[GIH][hapmap];0.86[TSI][hapmap];0.89[YRI][hapmap]
rs949930	1.00[CEU][hapmap];0.89[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
2	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
3	nsv1035107	chr7:65814901-66114919	Genic enhancers Strong transcription ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	nsv538909	chr7:65814901-66114919	Strong transcription Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	nsv888326	chr7:65825257-66066999	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv482441	chr7:65885824-66061788	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	esv1802195	chr7:65886451-65945211	Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv970514	chr7:65887884-65891263	Weak transcription Enhancers Strong transcription Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:32)

SNP	Gene	Cis/trans	Tissue	Source
rs6947339	ZNF117	cis	parietal	SCAN
rs6947339	GS1-124K5.4	cis	Stomach	GTEx
rs6947339	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs6947339	RNU6-96P	cis	Thyroid	GTEx
rs6947339	GS1-124K5.2	cis	Whole Blood	GTEx
rs6947339	GUSB	cis	parietal	SCAN
rs6947339	GS1-124K5.4	cis	Artery Aorta	GTEx
rs6947339	KCTD7	cis	parietal	SCAN
rs6947339	RAF1	trans	cerebellum	SCAN
rs6947339	TPST1	cis	lymphoblastoid	seeQTL
rs6947339	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs6947339	GS1-124K5.11	cis	Thyroid	GTEx
rs6947339	RP4-756H11.3	cis	Artery Tibial	GTEx
rs6947339	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs6947339	TPST1	cis	multi-tissue	Pritchard
rs6947339	GUSB	cis	cerebellum	SCAN
rs6947339	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs6947339	GTF2IRD1P1	cis	Thyroid	GTEx
rs6947339	GS1-124K5.4	cis	Skin Sun Exposed Lower leg	GTEx
rs6947339	CRCP	cis	parietal	SCAN
rs6947339	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs6947339	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs6947339	RABGEF1	cis	parietal	SCAN
rs6947339	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs6947339	GS1-124K5.4	cis	Esophagus Mucosa	GTEx
rs6947339	CRCP	cis	cerebellum	SCAN
rs6947339	RP4-756H11.3	cis	Thyroid	GTEx
rs6947339	RP4-756H11.3	cis	lung	GTEx
rs6947339	VKORC1L1	cis	multi-tissue	Pritchard
rs6947339	RABGEF1	cis	cerebellum	SCAN
rs6947339	LINC00174	cis	Thyroid	GTEx
rs6947339	ASL	cis	cerebellum	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65876200-65888600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:65877000-65888600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr7:65879000-65890000	Weak transcription	HSMM	muscle
4	chr7:65879000-65891800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr7:65879000-65893200	Weak transcription	Aorta	Aorta
6	chr7:65879000-65905600	Weak transcription	Lung	lung
7	chr7:65879000-65909000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr7:65879000-65922200	Weak transcription	Small Intestine	intestine
9	chr7:65879200-65888600	Weak transcription	Adipose Nuclei	Adipose
10	chr7:65879200-65889600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr7:65879200-65891400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr7:65879200-65893000	Weak transcription	Gastric	stomach
13	chr7:65879200-65893800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr7:65879200-65894600	Weak transcription	HMEC	breast
15	chr7:65879200-65894800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr7:65879200-65896000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr7:65879200-65902000	Weak transcription	Brain Substantia Nigra	brain
18	chr7:65879200-65904000	Weak transcription	Fetal Lung	lung
19	chr7:65879200-65907400	Weak transcription	Esophagus	oesophagus
20	chr7:65879200-65924600	Weak transcription	Brain Anterior Caudate	brain
21	chr7:65879200-65939800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr7:65879200-65946000	Weak transcription	NHEK	skin
23	chr7:65879200-65957600	Weak transcription	Psoas Muscle	Psoas
24	chr7:65879400-65889400	Weak transcription	Fetal Muscle Leg	muscle
25	chr7:65879400-65889600	Weak transcription	Primary T cells from cord blood	blood
26	chr7:65879400-65889800	Weak transcription	Ovary	ovary
27	chr7:65879400-65890800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr7:65879400-65891200	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr7:65879400-65891400	Weak transcription	Colonic Mucosa	Colon
30	chr7:65879400-65892600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr7:65879400-65900600	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr7:65879400-65901000	Weak transcription	Brain Angular Gyrus	brain
33	chr7:65879400-65901200	Weak transcription	Stomach Smooth Muscle	stomach
34	chr7:65879400-65909200	Weak transcription	Primary hematopoietic stem cells	blood
35	chr7:65879400-65914200	Weak transcription	Left Ventricle	heart
36	chr7:65879400-65914200	Weak transcription	GM12878-XiMat	blood
37	chr7:65879400-65917200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr7:65879400-65921000	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr7:65879400-65921400	Weak transcription	Fetal Kidney	kidney
40	chr7:65879600-65888600	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr7:65879600-65888800	Weak transcription	Fetal Intestine Small	intestine
42	chr7:65879600-65889600	Weak transcription	Fetal Intestine Large	intestine
43	chr7:65879600-65892200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr7:65879600-65893800	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr7:65879600-65895000	Weak transcription	Duodenum Mucosa	Duodenum
46	chr7:65879600-65899400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr7:65879600-65900600	Weak transcription	Brain Germinal Matrix	brain
48	chr7:65879600-65907600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr7:65879600-65913600	Weak transcription	Primary B cells from peripheral blood	blood
50	chr7:65879600-65919000	Weak transcription	Primary T helper cells PMA-I stimulated	--

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