Variant report

Variant	rs12701305
Chromosome Location	chr7:3995071-3995072
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1013492	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10227007	0.82[CEU][hapmap]
rs10230104	0.82[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs10260999	0.85[ASN][1000 genomes]
rs10264343	0.85[AMR][1000 genomes]
rs10277771	0.83[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];0.87[JPT][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11974050	0.97[ASN][1000 genomes]
rs11977815	0.93[CHD][hapmap];0.88[TSI][hapmap]
rs12534781	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12701279	0.82[CEU][hapmap];0.90[CHB][hapmap];0.85[AMR][1000 genomes]
rs12701280	0.90[CHB][hapmap];0.82[AMR][1000 genomes]
rs12701282	0.82[CHB][hapmap]
rs12701283	0.85[AMR][1000 genomes]
rs12701284	0.87[ASW][hapmap];0.82[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.83[LWK][hapmap];0.85[MKK][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes]
rs12701287	0.90[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap]
rs12701291	0.86[ASW][hapmap];0.86[CEU][hapmap];0.86[CHD][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes]
rs12701293	0.86[AMR][1000 genomes]
rs12701296	0.86[CEU][hapmap];0.82[CHB][hapmap];0.82[GIH][hapmap];0.83[LWK][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes]
rs12701311	0.95[CEU][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12701325	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17134054	0.81[CEU][hapmap]
rs17134098	0.86[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2010279	0.82[CHB][hapmap]
rs2016180	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs2040937	0.86[AMR][1000 genomes]
rs2044225	0.90[AMR][1000 genomes]
rs2068368	0.87[CEU][hapmap];0.90[CHD][hapmap];0.93[TSI][hapmap]
rs2120331	0.88[ASN][1000 genomes]
rs3801066	0.82[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3801067	0.82[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap];0.88[ASN][1000 genomes]
rs4720128	0.90[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4723267	0.90[CHB][hapmap]
rs4723268	0.82[CEU][hapmap]
rs4723269	0.82[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]
rs4723270	0.81[CEU][hapmap];0.88[CHB][hapmap];0.85[AMR][1000 genomes]
rs4723275	0.82[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes]
rs4723277	0.86[CEU][hapmap];0.90[CHB][hapmap]
rs4723284	0.86[TSI][hapmap]
rs62439587	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6462476	0.82[CEU][hapmap]
rs6462500	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6951851	0.90[TSI][hapmap]
rs6955390	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6965800	0.91[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6969705	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6974821	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6978757	0.91[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6980159	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6980313	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7776705	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7784194	0.82[CEU][hapmap];0.89[CHD][hapmap]
rs7786879	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7789580	0.82[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.81[AMR][1000 genomes]
rs7805988	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs968689	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021650	chr7:3665232-4577439	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1029406	chr7:3860894-4477095	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv538685	chr7:3860894-4477095	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1026410	chr7:3869104-4383606	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1025497	chr7:3905444-4176032	Enhancers Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv538686	chr7:3905444-4176032	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv433014	chr7:3910039-4054769	Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv464274	chr7:3955516-4613607	Weak transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv464275	chr7:3955516-4613607	Enhancers Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv464276	chr7:3955516-4613607	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv464277	chr7:3955516-4613607	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv464278	chr7:3955516-4613607	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv605939	chr7:3955516-4613607	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv1019086	chr7:3968656-4044519	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv538687	chr7:3968656-4044519	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv1019305	chr7:3991646-4276004	Enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	esv3360648	chr7:3992851-3995399	Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
18	esv3400892	chr7:3992976-3995174	Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12701305	WIPI2	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3987600-3995200	Weak transcription	Esophagus	oesophagus
2	chr7:3988400-4005400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr7:3988600-4010000	Weak transcription	Left Ventricle	heart
4	chr7:3988600-4032600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr7:3988800-4001600	Weak transcription	Right Atrium	heart
6	chr7:3989000-3995200	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr7:3989200-4013800	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr7:3989400-3997400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr7:3989400-4031000	Weak transcription	Right Ventricle	heart
10	chr7:3989800-4002400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr7:3989800-4020800	Weak transcription	Colon Smooth Muscle	Colon
12	chr7:3990000-3999800	Weak transcription	Fetal Brain Male	brain
13	chr7:3990200-3995400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr7:3990600-3995200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr7:3991200-3995200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr7:3991400-3995200	Weak transcription	Fetal Stomach	stomach
17	chr7:3991600-3995200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr7:3991600-3997800	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr7:3991600-4001400	Weak transcription	Stomach Smooth Muscle	stomach
20	chr7:3991800-3995800	Enhancers	HepG2	liver
21	chr7:3991800-4001400	Weak transcription	Fetal Brain Female	brain
22	chr7:3992000-3995200	Weak transcription	Fetal Lung	lung
23	chr7:3993200-3996400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr7:3994600-3995400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr7:3994600-3995400	Strong transcription	Aorta	Aorta
26	chr7:3994600-3995400	Strong transcription	Fetal Intestine Small	intestine
27	chr7:3994600-3995600	Enhancers	Lung	lung
28	chr7:3994600-3995600	Strong transcription	Pancreas	Pancrea
29	chr7:3994600-3995800	Enhancers	Fetal Thymus	thymus
30	chr7:3994600-3996000	Enhancers	Fetal Muscle Trunk	muscle
31	chr7:3994600-3997000	Enhancers	Fetal Muscle Leg	muscle
32	chr7:3994600-3997400	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr7:3994800-3995200	Enhancers	Brain Germinal Matrix	brain
34	chr7:3994800-3996000	Enhancers	GM12878-XiMat	blood
35	chr7:3994800-3996200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr7:3994800-3998200	Enhancers	Primary B cells from peripheral blood	blood
37	chr7:3995000-3995600	Enhancers	NHEK	skin
38	chr7:3995000-3996200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr7:3995000-3996200	Enhancers	HSMMtube	muscle
40	chr7:3995000-3996400	Enhancers	Muscle Satellite Cultured Cells	--
41	chr7:3995000-3996400	Enhancers	HSMM	muscle
42	chr7:3995000-3997000	Enhancers	Spleen	Spleen

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