Variant report

Variant	rs12701296
Chromosome Location	chr7:3970800-3970801
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	chr7:3966955..3968724-chr7:3970667..3972517,2	MCF-7	breast:

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1013492	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10227007	0.95[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10230104	0.95[CEU][hapmap];0.83[CHD][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10240160	0.94[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10264343	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10264360	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10277771	0.83[MEX][hapmap];0.81[TSI][hapmap]
rs11977815	0.83[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12534781	0.83[AMR][1000 genomes]
rs12701279	0.95[CEU][hapmap];0.93[JPT][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12701280	0.91[CEU][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12701281	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12701282	0.90[CEU][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12701283	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12701284	0.87[ASW][hapmap];0.95[CEU][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];0.91[LWK][hapmap];0.81[TSI][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12701287	0.85[CEU][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.83[LWK][hapmap];0.87[ASN][1000 genomes]
rs12701291	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.84[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12701293	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12701305	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	0.82[CEU][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes]
rs12701325	0.85[AMR][1000 genomes]
rs17134054	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17134098	0.82[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes]
rs2010279	0.91[CEU][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2016180	0.95[CEU][hapmap];0.93[JPT][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2040937	0.91[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2044224	0.91[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2044225	0.93[JPT][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2068368	0.91[CEU][hapmap];0.83[CHD][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3735305	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3801067	0.88[MEX][hapmap];0.80[AMR][1000 genomes]
rs4720116	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4720128	0.81[TSI][hapmap]
rs4723267	0.91[CEU][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs4723268	0.95[CEU][hapmap];0.83[AMR][1000 genomes]
rs4723269	0.95[CEU][hapmap];0.83[CHD][hapmap];0.93[JPT][hapmap];0.91[TSI][hapmap];0.86[ASN][1000 genomes]
rs4723270	0.95[CEU][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4723275	0.95[CEU][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4723277	0.95[CEU][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4723284	0.87[CEU][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6462476	0.95[CEU][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6951851	0.87[CEU][hapmap];0.84[CHB][hapmap];0.90[CHD][hapmap];0.93[JPT][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6965800	0.87[CEU][hapmap];0.82[CHB][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs6978757	0.87[CEU][hapmap];0.82[CHB][hapmap];0.83[TSI][hapmap]
rs7784194	0.95[CEU][hapmap];0.83[CHD][hapmap];0.93[JPT][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7789580	0.95[CEU][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7801639	0.80[MEX][hapmap]
rs7805988	0.87[CEU][hapmap];0.82[CHB][hapmap]
rs7810787	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 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	nsv518377	chr7:3939055-3978342	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv1030082	chr7:3941203-3986403	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv1020222	chr7:3946655-3985756	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv1027500	chr7:3949954-3986403	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv1024445	chr7:3954131-3982653	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12701296	WIPI2	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3936800-3974200	Weak transcription	Aorta	Aorta
2	chr7:3962000-3972600	Weak transcription	Spleen	Spleen
3	chr7:3962000-3982400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr7:3964400-3970800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr7:3965400-3974200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr7:3966600-3974200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr7:3969400-3972000	Enhancers	Fetal Brain Male	brain
8	chr7:3969600-3974400	Weak transcription	Fetal Muscle Trunk	muscle
9	chr7:3970000-3970800	Weak transcription	Fetal Brain Female	brain
10	chr7:3970000-3971800	Weak transcription	Pancreas	Pancrea
11	chr7:3970800-3971000	Enhancers	Fetal Brain Female	brain
12	chr7:3970800-3971800	Enhancers	Pancreatic Islets	Pancreatic Islet

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