Variant report

Variant	rs2711656
Chromosome Location	chr12:60165991-60165992
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10431557	0.85[CHB][hapmap]
rs10506398	0.85[CHB][hapmap]
rs10506399	0.90[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs10877338	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10877342	0.81[CEU][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11173124	0.81[ASN][1000 genomes]
rs11173126	0.95[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs11173133	0.82[CHB][hapmap];0.92[ASN][1000 genomes]
rs11173134	0.92[ASN][1000 genomes]
rs11173137	0.89[ASN][1000 genomes]
rs11173158	0.83[ASN][1000 genomes]
rs11173159	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs11173164	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12227214	0.91[ASN][1000 genomes]
rs12227244	0.90[CHB][hapmap]
rs12227270	0.85[CHB][hapmap]
rs12231311	0.95[CHB][hapmap];0.90[ASN][1000 genomes]
rs12231693	0.95[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs12231740	0.85[CHB][hapmap]
rs12232002	0.95[CHB][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs12812799	0.92[ASN][1000 genomes]
rs12816935	0.89[CHB][hapmap]
rs17572877	0.83[ASN][1000 genomes]
rs17572912	0.83[ASN][1000 genomes]
rs17649424	0.95[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs17650311	0.95[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs1795884	0.89[ASW][hapmap];0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1795896	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2365316	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2365317	0.83[ASN][1000 genomes]
rs2365318	0.83[ASN][1000 genomes]
rs2706295	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2706306	0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.88[MKK][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2706309	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2706319	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2711655	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2711659	0.89[ASW][hapmap];0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2711668	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2711670	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2711672	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2711677	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2711691	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2886339	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34264510	0.92[ASN][1000 genomes]
rs34639075	0.83[ASN][1000 genomes]
rs34785387	0.92[ASN][1000 genomes]
rs35365387	0.92[ASN][1000 genomes]
rs35518979	0.90[ASN][1000 genomes]
rs3763980	0.95[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs4583011	0.92[ASN][1000 genomes]
rs56682442	0.92[ASN][1000 genomes]
rs61174819	0.92[ASN][1000 genomes]
rs6581274	0.83[ASN][1000 genomes]
rs66802005	0.92[ASN][1000 genomes]
rs66861118	0.92[ASN][1000 genomes]
rs68028492	0.90[ASN][1000 genomes]
rs7133415	0.95[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs7303876	0.95[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs7307330	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7978598	0.83[ASN][1000 genomes]
rs7979504	0.83[ASN][1000 genomes]
rs9705733	0.90[ASN][1000 genomes]
rs9788077	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869425	chr12:59746898-60479741	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS 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	22 gene(s)	inside rSNPs	diseases
2	esv3365928	chr12:60042531-60343212	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv899132	chr12:60087572-60211476	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv899133	chr12:60135504-60202218	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv899134	chr12:60141518-60263723	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv899135	chr12:60156046-60228610	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv559101	chr12:60164408-60202218	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv559102	chr12:60164408-60221898	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv2058503	chr12:60165991-60165992	Strong transcription Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2711656	COPZ1	cis	parietal	SCAN
rs2711656	SDR9C7	cis	cerebellum	SCAN
rs2711656	SLC16A7	Cis_1M	lymphoblastoid	RTeQTL
rs2711656	KIF5A	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:60100000-60175200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr12:60124000-60168800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr12:60130800-60172200	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr12:60131000-60186000	Weak transcription	Pancreas	Pancrea
5	chr12:60138600-60168400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr12:60138800-60173200	Weak transcription	Aorta	Aorta
7	chr12:60152000-60182200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr12:60159000-60168400	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr12:60159000-60172000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr12:60159800-60186400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr12:60160400-60186000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr12:60161200-60168800	Weak transcription	Adipose Nuclei	Adipose
13	chr12:60161200-60181600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr12:60161200-60186800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:60161400-60167800	Weak transcription	Primary T cells from cord blood	blood
16	chr12:60161400-60168400	Weak transcription	Left Ventricle	heart
17	chr12:60161400-60168600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr12:60161400-60176400	Weak transcription	GM12878-XiMat	blood
19	chr12:60161600-60168600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr12:60161600-60169000	Weak transcription	Dnd41	blood
21	chr12:60161600-60176400	Weak transcription	Primary hematopoietic stem cells	blood
22	chr12:60161800-60186000	Weak transcription	Lung	lung
23	chr12:60162400-60169200	Weak transcription	Right Ventricle	heart
24	chr12:60162600-60175000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr12:60162600-60186000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr12:60162800-60184000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr12:60162800-60186000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr12:60163200-60168600	Weak transcription	Primary B cells from peripheral blood	blood
29	chr12:60163800-60174400	Weak transcription	NHDF-Ad	bronchial
30	chr12:60164400-60174600	Weak transcription	Fetal Thymus	thymus
31	chr12:60164800-60167200	Strong transcription	Primary B cells from cord blood	blood
32	chr12:60165600-60167000	Strong transcription	Primary T helper cells fromperipheralblood	blood

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