Variant report

Variant	rs12701311
Chromosome Location	chr7:3997993-3997994
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:3996452..3999327-chr7:4001947..4004712,2	MCF-7	breast:
2	chr7:3997502..3999160-chr7:4000624..4002138,2	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1013492	0.83[AMR][1000 genomes]
rs10227007	0.87[CEU][hapmap]
rs10230104	0.87[CEU][hapmap];0.90[GIH][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs10240160	0.84[CEU][hapmap]
rs10277771	0.87[CEU][hapmap];0.92[GIH][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs11977815	0.83[CEU][hapmap];0.90[GIH][hapmap];0.88[TSI][hapmap]
rs12534781	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12536527	0.85[CHB][hapmap];0.96[CHD][hapmap];0.82[JPT][hapmap]
rs12701277	0.85[CHB][hapmap]
rs12701282	0.81[CEU][hapmap]
rs12701284	0.86[TSI][hapmap]
rs12701291	0.82[CEU][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes]
rs12701293	0.81[AMR][1000 genomes]
rs12701296	0.82[CEU][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes]
rs12701305	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]
rs17134098	0.82[CEU][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2016180	0.87[CEU][hapmap]
rs2040937	0.82[CEU][hapmap];0.81[AMR][1000 genomes]
rs2044224	0.82[CEU][hapmap]
rs2044225	0.83[AMR][1000 genomes]
rs2068368	0.91[CEU][hapmap];0.92[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]
rs3801066	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs3801067	0.90[GIH][hapmap];0.93[TSI][hapmap]
rs4720128	0.82[CEU][hapmap];0.92[GIH][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs4723267	0.82[CEU][hapmap]
rs4723269	0.87[CEU][hapmap];0.92[GIH][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs4723275	0.81[CHD][hapmap];0.81[TSI][hapmap]
rs4723277	0.91[CEU][hapmap]
rs4723284	0.86[TSI][hapmap]
rs62439587	0.89[EUR][1000 genomes]
rs6462476	0.87[CEU][hapmap]
rs6462500	0.85[EUR][1000 genomes]
rs6951851	0.87[GIH][hapmap];0.90[TSI][hapmap]
rs6955390	0.86[EUR][1000 genomes]
rs6965800	0.87[CEU][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs6969705	0.87[EUR][1000 genomes]
rs6974821	0.85[EUR][1000 genomes]
rs6978757	0.87[CEU][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs6980159	0.85[EUR][1000 genomes]
rs6980313	0.85[EUR][1000 genomes]
rs7776705	0.84[EUR][1000 genomes]
rs7784194	0.87[CEU][hapmap];0.90[GIH][hapmap]
rs7786879	0.85[EUR][1000 genomes]
rs7789580	0.81[CHD][hapmap]
rs7805988	0.87[CEU][hapmap]
rs968689	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12701311	WIPI2	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3988400-4005400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:3988600-4010000	Weak transcription	Left Ventricle	heart
3	chr7:3988600-4032600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr7:3988800-4001600	Weak transcription	Right Atrium	heart
5	chr7:3989200-4013800	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr7:3989400-4031000	Weak transcription	Right Ventricle	heart
7	chr7:3989800-4002400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr7:3989800-4020800	Weak transcription	Colon Smooth Muscle	Colon
9	chr7:3990000-3999800	Weak transcription	Fetal Brain Male	brain
10	chr7:3991600-4001400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr7:3991800-4001400	Weak transcription	Fetal Brain Female	brain
12	chr7:3994800-3998200	Enhancers	Primary B cells from peripheral blood	blood
13	chr7:3995200-4007400	Weak transcription	Brain Germinal Matrix	brain
14	chr7:3995400-3998600	Weak transcription	Aorta	Aorta
15	chr7:3995400-4001800	Weak transcription	Fetal Intestine Small	intestine
16	chr7:3995600-4001400	Weak transcription	Pancreas	Pancrea
17	chr7:3995800-4001400	Weak transcription	Fetal Kidney	kidney
18	chr7:3995800-4001400	Weak transcription	Fetal Lung	lung
19	chr7:3995800-4001400	Weak transcription	HepG2	liver
20	chr7:3996200-4000000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr7:3996200-4007200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr7:3996200-4017200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr7:3996400-3999800	Weak transcription	Fetal Thymus	thymus
24	chr7:3996400-4001800	Weak transcription	Fetal Stomach	stomach
25	chr7:3996400-4015800	Weak transcription	HSMM	muscle
26	chr7:3996400-4037600	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr7:3996600-3998600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr7:3997000-3998600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr7:3997000-3999400	Weak transcription	Fetal Muscle Leg	muscle
30	chr7:3997000-4001400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr7:3997000-4006400	Weak transcription	Spleen	Spleen
32	chr7:3997000-4019400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr7:3997400-3998000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr7:3997400-3998600	Weak transcription	Gastric	stomach
35	chr7:3997600-3998000	Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr7:3997800-3998400	Enhancers	Cortex derived primary cultured neurospheres	brain

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