Variant report

Variant	rs12701287
Chromosome Location	chr7:3960126-3960127
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:3959768..3961980-chr7:3963709..3965719,2	K562	blood:
2	chr7:3958497..3961306-chr7:3967336..3968851,2	K562	blood:
3	chr7:3959798..3963581-chr7:3965288..3967967,3	MCF-7	breast:
4	chr7:3953782..3957860-chr7:3959035..3961864,3	K562	blood:
5	chr7:3958497..3961306-chr7:3966157..3968851,3	K562	blood:

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1013492	0.87[ASN][1000 genomes]
rs10227007	0.81[CEU][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs10230104	0.81[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10240160	0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs10260999	0.86[ASN][1000 genomes]
rs10277771	0.81[CHB][hapmap];0.85[CHD][hapmap]
rs11977815	0.83[CHD][hapmap]
rs12530629	0.80[ASN][1000 genomes]
rs12536527	0.81[CHD][hapmap];0.82[GIH][hapmap]
rs12701277	0.84[CEU][hapmap];0.82[AMR][1000 genomes]
rs12701279	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12701280	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12701281	0.99[ASN][1000 genomes]
rs12701282	0.91[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12701283	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12701284	0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.83[MEX][hapmap];1.00[ASN][1000 genomes]
rs12701291	0.85[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];0.91[LWK][hapmap];0.85[ASN][1000 genomes]
rs12701293	0.88[ASN][1000 genomes]
rs12701296	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]
rs12701305	0.90[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap]
rs17134054	0.84[CEU][hapmap];0.83[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs17134098	0.90[CHB][hapmap]
rs2010279	0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2016180	0.81[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2040937	0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs2044224	0.81[JPT][hapmap]
rs2044225	0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs2068368	0.83[CHB][hapmap];0.80[CHD][hapmap]
rs2120331	0.83[ASN][1000 genomes]
rs3801066	0.81[CHB][hapmap]
rs3801067	0.91[CHB][hapmap];0.89[CHD][hapmap];0.83[ASN][1000 genomes]
rs4720116	0.95[ASN][1000 genomes]
rs4720128	0.81[CHB][hapmap];0.85[CHD][hapmap]
rs4723267	0.81[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4723268	0.85[CEU][hapmap]
rs4723269	0.81[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4723270	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4723275	0.81[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4723277	0.81[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4723284	0.83[CHD][hapmap]
rs6462476	0.81[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs6951851	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs6965800	0.90[CHB][hapmap];0.85[CHD][hapmap]
rs6968948	0.84[CHB][hapmap]
rs6978757	0.90[CHB][hapmap];0.85[CHD][hapmap]
rs7784194	0.81[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7789580	0.81[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.99[ASN][1000 genomes]
rs7805988	0.90[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:19 , 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	esv9938	chr7:3959832-3960502	Weak transcription Strong transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12701287	EIF2AK1	cis	cerebellum	SCAN
rs12701287	WIPI2	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3936800-3974200	Weak transcription	Aorta	Aorta
2	chr7:3952200-3960600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr7:3952400-3963200	Weak transcription	Lung	lung
4	chr7:3956200-3961600	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr7:3956200-3961600	Weak transcription	Adipose Nuclei	Adipose
6	chr7:3956200-3961600	Weak transcription	NHEK	skin
7	chr7:3956200-3961800	Weak transcription	Brain Angular Gyrus	brain
8	chr7:3956200-3961800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr7:3956400-3961400	Weak transcription	NH-A	brain
10	chr7:3956400-3961800	Weak transcription	Brain Hippocampus Middle	brain
11	chr7:3956400-3961800	Weak transcription	Brain Substantia Nigra	brain
12	chr7:3957000-3963600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr7:3957200-3961800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr7:3957400-3961600	Weak transcription	HepG2	liver
15	chr7:3957400-3961600	Weak transcription	HSMMtube	muscle
16	chr7:3957600-3961600	Weak transcription	HUVEC	blood vessel
17	chr7:3958600-3961600	Weak transcription	Spleen	Spleen
18	chr7:3959000-3960400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr7:3959200-3961600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr7:3959600-3960200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr7:3959800-3961400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr7:3960000-3961600	Weak transcription	Pancreas	Pancrea

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