Variant report

Variant	rs3112527
Chromosome Location	chr17:16248906-16248907
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:16248670-16249277	GM12892	blood:	n/a	n/a
2	POLR2A	chr17:16248833-16249535	HepG2	liver:	n/a	n/a
3	POLR2A	chr17:16248780-16251384	HepG2	liver:	n/a	n/a
4	FOSL2	chr17:16248868-16249267	HepG2	liver:	n/a	chr17:16249250-16249259
5	BCL3	chr17:16248745-16249688	A549	lung:	n/a	n/a
6	POLR2A	chr17:16248856-16249219	K562	blood:	n/a	n/a
7	POLR2A	chr17:16248881-16248975	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr17:16248846-16249137	K562	blood:	n/a	n/a
9	POLR2A	chr17:16248880-16249158	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr17:16248830-16249777	A549	lung:	n/a	n/a
11	POLR2A	chr17:16248707-16249445	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr17:16247451-16250670	K562	blood:	n/a	n/a
13	POLR2A	chr17:16248732-16249220	PFSK-1	brain:	n/a	n/a
14	POLR2A	chr17:16248661-16249117	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr17:16248110-16249535	HepG2	liver:	n/a	n/a
16	POLR2A	chr17:16248840-16249204	K562	blood:	n/a	n/a
17	POLR2A	chr17:16248642-16249900	HepG2	liver:	n/a	n/a
18	POLR2A	chr17:16248649-16249215	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr17:16248692-16249776	HepG2	liver:	n/a	n/a
20	POLR2A	chr17:16248850-16249189	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr17:16248731-16249180	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr17:16248839-16249202	Hela-S3	cervix:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:16246064..16249335-chr17:16283382..16285642,3	MCF-7	breast:
2	chr17:16244008..16245759-chr17:16248063..16249600,2	K562	blood:
3	chr17:16247522..16250151-chr17:16316906..16319854,2	K562	blood:

No data

Variant related genes	Relation type
CENPV	TF binding region
ENSG00000170315	Chromatin interaction
ENSG00000187688	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	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs11654658	0.81[GIH][hapmap]
rs11656811	0.81[GIH][hapmap]
rs11868284	0.81[GIH][hapmap]
rs12603712	0.81[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	0.92[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];0.81[MEX][hapmap]
rs3112513	0.90[GIH][hapmap];0.81[MEX][hapmap]
rs3112518	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112520	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3112521	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112522	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3112524	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]
rs3112525	0.94[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];0.86[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	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	0.90[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];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]
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
rs3112527	ZSWIM7	cis	Muscle Skeletal	GTEx
rs3112527	CENPV	cis	Brain Pons	GTEx
rs3112527	TRPV2	cis	Frontal Cortex	GTEx
rs3112527	CENPV	cis	Temporal Cortex	GTEx
rs3112527	ELAC2	cis	parietal	SCAN
rs3112527	ADORA2B	cis	Adipose Subcutaneous	GTEx
rs3112527	TTC19	Cis_1M	lymphoblastoid	RTeQTL
rs3112527	ADORA2B	cis	Esophagus Muscularis	GTEx
rs3112527	TRPV2	cis	parietal	SCAN
rs3112527	PRR6	cis	multi-tissue	Pritchard
rs3112527	ZSWIM7	Cis_1M	lymphoblastoid	RTeQTL
rs3112527	CENPV	cis	Frontal Cortex	GTEx
rs3112527	CENPV	cis	Artery Tibial	GTEx
rs3112527	CENPV	cis	parietal	SCAN
rs3112527	ADORA2B	cis	Artery Tibial	GTEx

Chromatin state (count:117 , 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	chr17:16245600-16249400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr17:16245600-16251800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr17:16245600-16251800	Strong transcription	Fetal Thymus	thymus
32	chr17:16245600-16253000	Strong transcription	Primary B cells from peripheral blood	blood
33	chr17:16245600-16253000	Strong transcription	Brain Germinal Matrix	brain
34	chr17:16245600-16253000	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr17:16245600-16253200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr17:16245600-16253200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr17:16245600-16253400	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr17:16245600-16253400	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr17:16245600-16253400	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr17:16245600-16253400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr17:16245600-16253400	Strong transcription	Fetal Intestine Large	intestine
42	chr17:16245600-16253400	Strong transcription	Fetal Muscle Trunk	muscle
43	chr17:16245600-16253400	Strong transcription	Fetal Stomach	stomach
44	chr17:16245600-16253600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr17:16245600-16253600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr17:16245600-16253600	Strong transcription	A549	lung
47	chr17:16245600-16254200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr17:16245800-16249600	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr17:16245800-16250600	Strong transcription	Brain Anterior Caudate	brain
50	chr17:16245800-16250800	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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