Variant report

Variant	rs17650311
Chromosome Location	chr12:60175605-60175606
allele	C/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	0.91[CHB][hapmap];0.85[GIH][hapmap]
rs10506398	0.91[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap]
rs10506399	0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877338	0.95[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs10877342	0.83[CHD][hapmap]
rs11173124	0.86[ASN][1000 genomes]
rs11173126	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11173133	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11173134	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11173137	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11173158	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11173159	0.90[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12227214	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12227244	0.86[CEU][hapmap];0.90[CHB][hapmap]
rs12227270	0.91[CHB][hapmap]
rs12231311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12231693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12231740	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs12232002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12812799	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12816935	0.95[CEU][hapmap];0.94[CHB][hapmap];0.80[EUR][1000 genomes]
rs17572877	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17572912	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17649424	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1795884	0.91[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs1795896	0.95[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs2365317	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2365318	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2706295	0.90[ASN][1000 genomes]
rs2706306	0.95[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs2706309	0.95[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs2706319	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2711655	0.95[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs2711656	0.95[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs2711659	0.90[CHB][hapmap];0.88[CHD][hapmap];0.90[ASN][1000 genomes]
rs2711668	0.95[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs2711670	0.89[ASN][1000 genomes]
rs2711672	0.89[ASN][1000 genomes]
rs2711677	0.89[ASN][1000 genomes]
rs2711691	0.90[ASN][1000 genomes]
rs34264510	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34639075	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34785387	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35218918	0.84[ASN][1000 genomes]
rs35365387	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35518979	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35971116	0.95[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs3763980	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4583011	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56682442	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61174819	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6581274	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66802005	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66861118	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs68028492	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7133415	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7136019	0.81[EUR][1000 genomes]
rs7303876	1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73111880	0.90[AFR][1000 genomes]
rs7979504	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9705733	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9788077	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs995342	0.85[CEU][hapmap]

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	esv275119	chr12:60169887-60176579	Enhancers Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17650311	KIF5A	cis	cerebellum	SCAN
rs17650311	SLC16A7	cis	lymphoblastoid	seeQTL
rs17650311	SLC16A7	Cis_1M	lymphoblastoid	RTeQTL
rs17650311	SLC16A7	cis	multi-tissue	Pritchard

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:60131000-60186000	Weak transcription	Pancreas	Pancrea
2	chr12:60152000-60182200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr12:60159800-60186400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr12:60160400-60186000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr12:60161200-60181600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr12:60161200-60186800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr12:60161400-60176400	Weak transcription	GM12878-XiMat	blood
8	chr12:60161600-60176400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr12:60161800-60186000	Weak transcription	Lung	lung
10	chr12:60162600-60186000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr12:60162800-60184000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr12:60162800-60186000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr12:60166600-60177000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr12:60167000-60177400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr12:60167800-60177400	Weak transcription	Ovary	ovary
16	chr12:60169200-60175800	Weak transcription	Primary B cells from peripheral blood	blood
17	chr12:60169200-60178000	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr12:60169200-60178200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr12:60169200-60187000	Weak transcription	Primary B cells from cord blood	blood
20	chr12:60169400-60187600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr12:60169400-60189200	Weak transcription	Dnd41	blood
22	chr12:60173000-60176800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr12:60173400-60189400	Weak transcription	Left Ventricle	heart
24	chr12:60174800-60186000	Weak transcription	Adipose Nuclei	Adipose
25	chr12:60175000-60176000	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr12:60175400-60176000	Strong transcription	Primary T cells from cord blood	blood
27	chr12:60175600-60179600	Weak transcription	Primary T helper cells PMA-I stimulated	--

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