Variant report

Variant	rs3112524
Chromosome Location	chr17:16245778-16245779
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	chr17:16244686..16247479-chr17:16252981..16254957,2	K562	blood:
2	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: 49 )
Associated
traits (count: 16 )

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

rs_ID	r²[population]
rs11653585	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs11654658	0.81[GIH][hapmap]
rs11656811	0.81[GIH][hapmap]
rs11868284	0.81[GIH][hapmap]
rs12603712	0.88[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	0.99[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	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112520	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3112521	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112522	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3112525	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[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];0.87[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[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	0.85[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	0.82[CEU][hapmap];0.83[TSI][hapmap];0.90[EUR][1000 genomes]
rs8071515	0.98[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]
rs917609	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]
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:5 , 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

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs3112524	CENPV	cis	Frontal Cortex	GTEx
rs3112524	ZSWIM7	Cis_1M	lymphoblastoid	RTeQTL
rs3112524	ZSWIM7	cis	Muscle Skeletal	GTEx
rs3112524	CENPV	cis	Artery Tibial	GTEx
rs3112524	ELAC2	cis	parietal	SCAN
rs3112524	CENPV	cis	Temporal Cortex	GTEx
rs3112524	PRR6	cis	multi-tissue	Pritchard
rs3112524	ADORA2B	cis	Artery Tibial	GTEx
rs3112524	CENPV	cis	Brain Pons	GTEx
rs3112524	CENPV	cis	parietal	SCAN
rs3112524	ADORA2B	cis	Adipose Subcutaneous	GTEx
rs3112524	ADORA2B	cis	Esophagus Muscularis	GTEx
rs3112524	PIGL	cis	multi-tissue	Pritchard
rs3112524	TRPV2	cis	parietal	SCAN
rs3112524	TTC19	Cis_1M	lymphoblastoid	RTeQTL
rs3112524	TRPV2	cis	Frontal Cortex	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16201600-16246400	Weak transcription	Fetal Brain Male	brain
2	chr17:16206000-16245800	Weak transcription	Brain Anterior Caudate	brain
3	chr17:16206000-16246000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr17:16214600-16255200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr17:16217000-16246000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr17:16217200-16255200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr17:16219200-16246000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr17:16225800-16245800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr17:16229400-16255600	Weak transcription	Esophagus	oesophagus
10	chr17:16230200-16246000	Weak transcription	Spleen	Spleen
11	chr17:16230400-16246000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr17:16230400-16246200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr17:16230400-16253600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr17:16230400-16255000	Weak transcription	Primary B cells from cord blood	blood
15	chr17:16230400-16255200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr17:16230400-16255200	Weak transcription	Brain Substantia Nigra	brain
17	chr17:16230600-16245800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr17:16230600-16245800	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr17:16230600-16245800	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr17:16230600-16245800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr17:16230600-16245800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr17:16230600-16246000	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr17:16230600-16246000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr17:16230600-16246000	Weak transcription	Brain Hippocampus Middle	brain
25	chr17:16230600-16246000	Weak transcription	Dnd41	blood
26	chr17:16230600-16246400	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr17:16230600-16250800	Weak transcription	Brain Angular Gyrus	brain
28	chr17:16230600-16254200	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr17:16230600-16255200	Weak transcription	Colon Smooth Muscle	Colon
30	chr17:16230600-16255200	Weak transcription	HSMMtube	muscle
31	chr17:16230800-16245800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr17:16230800-16254600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr17:16231000-16245800	Weak transcription	Pancreas	Pancrea
34	chr17:16231000-16246000	Weak transcription	Ovary	ovary
35	chr17:16233000-16245800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr17:16233000-16245800	Weak transcription	Stomach Smooth Muscle	stomach
37	chr17:16233000-16246000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr17:16233200-16246000	Weak transcription	Brain Cingulate Gyrus	brain
39	chr17:16233200-16255400	Weak transcription	Right Atrium	heart
40	chr17:16233400-16245800	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr17:16233400-16245800	Weak transcription	Osteobl	bone
42	chr17:16237000-16245800	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr17:16238000-16255000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr17:16239400-16245800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr17:16239800-16245800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr17:16240200-16250400	Weak transcription	NH-A	brain
47	chr17:16240800-16254800	Weak transcription	HSMM	muscle
48	chr17:16241000-16246200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr17:16241000-16255000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr17:16241400-16252400	Weak transcription	HUVEC	blood vessel

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