Variant report

Variant	rs917609
Chromosome Location	chr17:16246608-16246609
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:16244686..16247479-chr17:16252981..16254957,2	K562	blood:
2	chr17:16246064..16249335-chr17:16283382..16285642,3	MCF-7	breast:
3	chr17:16244398..16248540-chr17:16283211..16286242,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000265401	Chromatin interaction
ENSG00000166582	Chromatin interaction
ENSG00000170315	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11653585	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs11654658	0.81[GIH][hapmap]
rs11656811	0.81[GIH][hapmap]
rs11868284	0.81[GIH][hapmap]
rs12603712	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12948680	0.84[AMR][1000 genomes]
rs12949375	0.80[ASN][1000 genomes]
rs2014604	0.90[GIH][hapmap]
rs2074995	0.87[CHB][hapmap]
rs2109262	0.81[GIH][hapmap]
rs3095166	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3095174	0.93[EUR][1000 genomes]
rs3112511	0.90[GIH][hapmap]
rs3112513	0.90[GIH][hapmap]
rs3112518	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112520	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3112521	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112522	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3112524	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112525	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112526	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3112527	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3785621	0.88[GIH][hapmap]
rs3785623	0.88[GIH][hapmap]
rs3785626	0.81[GIH][hapmap]
rs4791665	0.90[GIH][hapmap]
rs4792728	0.81[GIH][hapmap]
rs4792731	0.81[GIH][hapmap]
rs62074191	0.92[EUR][1000 genomes]
rs62074192	0.87[EUR][1000 genomes]
rs62074224	0.82[EUR][1000 genomes]
rs714285	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7219687	0.90[GIH][hapmap]
rs72838750	0.89[EUR][1000 genomes]
rs7477	0.83[TSI][hapmap];0.90[EUR][1000 genomes]
rs8071515	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8071642	0.91[ASN][1000 genomes]
rs8073259	0.83[GIH][hapmap]
rs8074246	0.93[EUR][1000 genomes]
rs9747806	0.82[EUR][1000 genomes]
rs9797249	0.80[EUR][1000 genomes]
rs9890539	0.81[GIH][hapmap];0.84[TSI][hapmap]
rs9907546	0.94[EUR][1000 genomes]
rs9944524	0.81[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934185	chr17:15552960-16551197	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	190 gene(s)	inside rSNPs	diseases
2	esv3330182	chr17:15652014-16569534	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
3	esv3446844	chr17:15654843-16572246	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
4	nsv1063459	chr17:15804228-16543593	Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
5	nsv1063764	chr17:16171649-16662914	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	120 gene(s)	inside rSNPs	diseases
6	nsv1061463	chr17:16245878-16490691	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	99 gene(s)	inside rSNPs	diseases
7	nsv543216	chr17:16245878-16490691	Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	99 gene(s)	inside rSNPs	diseases
8	nsv962266	chr17:16245920-16260306	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs917609	CENPV	cis	Brain Pons	GTEx
rs917609	CENPV	cis	Artery Tibial	GTEx
rs917609	ADORA2B	cis	Esophagus Muscularis	GTEx
rs917609	ADORA2B	cis	Artery Tibial	GTEx
rs917609	TTC19	Cis_1M	lymphoblastoid	RTeQTL
rs917609	CENPV	cis	Temporal Cortex	GTEx
rs917609	PRR6	cis	multi-tissue	Pritchard
rs917609	ZSWIM7	cis	Muscle Skeletal	GTEx
rs917609	CENPV	cis	parietal	SCAN
rs917609	TRPV2	cis	parietal	SCAN
rs917609	ADORA2B	cis	Adipose Subcutaneous	GTEx
rs917609	CENPV	cis	Frontal Cortex	GTEx
rs917609	ELAC2	cis	parietal	SCAN
rs917609	TRPV2	cis	Frontal Cortex	GTEx
rs917609	ZSWIM7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16214600-16255200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr17:16217200-16255200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr17:16229400-16255600	Weak transcription	Esophagus	oesophagus
4	chr17:16230400-16253600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr17:16230400-16255000	Weak transcription	Primary B cells from cord blood	blood
6	chr17:16230400-16255200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr17:16230400-16255200	Weak transcription	Brain Substantia Nigra	brain
8	chr17:16230600-16250800	Weak transcription	Brain Angular Gyrus	brain
9	chr17:16230600-16254200	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr17:16230600-16255200	Weak transcription	Colon Smooth Muscle	Colon
11	chr17:16230600-16255200	Weak transcription	HSMMtube	muscle
12	chr17:16230800-16254600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr17:16233200-16255400	Weak transcription	Right Atrium	heart
14	chr17:16238000-16255000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr17:16240200-16250400	Weak transcription	NH-A	brain
16	chr17:16240800-16254800	Weak transcription	HSMM	muscle
17	chr17:16241000-16255000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr17:16241400-16252400	Weak transcription	HUVEC	blood vessel
19	chr17:16242000-16255000	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr17:16242200-16255200	Weak transcription	NHEK	skin
21	chr17:16242400-16250400	Weak transcription	Small Intestine	intestine
22	chr17:16242800-16255000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr17:16243800-16250800	Strong transcription	Thymus	Thymus
24	chr17:16244400-16249600	Strong transcription	Fetal Lung	lung
25	chr17:16244600-16252600	Weak transcription	Psoas Muscle	Psoas
26	chr17:16244600-16254800	Weak transcription	Stomach Mucosa	stomach
27	chr17:16244800-16253200	Strong transcription	Fetal Intestine Small	intestine
28	chr17:16245200-16255200	Weak transcription	NHDF-Ad	bronchial
29	chr17:16245400-16248000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr17:16245600-16246800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr17:16245600-16246800	Strong transcription	HepG2	liver
32	chr17:16245600-16247600	Strong transcription	NHLF	lung
33	chr17:16245600-16247800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr17:16245600-16248000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr17:16245600-16248000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
36	chr17:16245600-16248000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr17:16245600-16248000	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr17:16245600-16248000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr17:16245600-16248000	Strong transcription	Fetal Muscle Leg	muscle
40	chr17:16245600-16248000	Strong transcription	Left Ventricle	heart
41	chr17:16245600-16248200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr17:16245600-16248200	Strong transcription	Brain Inferior Temporal Lobe	brain
43	chr17:16245600-16248200	Strong transcription	Duodenum Mucosa	Duodenum
44	chr17:16245600-16249400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr17:16245600-16251800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr17:16245600-16251800	Strong transcription	Fetal Thymus	thymus
47	chr17:16245600-16253000	Strong transcription	Primary B cells from peripheral blood	blood
48	chr17:16245600-16253000	Strong transcription	Brain Germinal Matrix	brain
49	chr17:16245600-16253000	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr17:16245600-16253200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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