Variant report

Variant	rs17093738
Chromosome Location	chr14:71586648-71586649
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:71582880..71584385-chr14:71586431..71588999,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1012725	0.87[ASW][hapmap];0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12100737	0.82[ASW][hapmap]
rs12323786	0.84[JPT][hapmap]
rs17108804	0.81[ASW][hapmap]
rs17108808	0.87[AMR][1000 genomes]
rs17108862	0.89[AMR][1000 genomes]
rs17109053	0.90[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2158996	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2158997	0.82[ASW][hapmap]
rs221909	0.80[AMR][1000 genomes]
rs221921	0.80[AMR][1000 genomes]
rs221922	0.80[AMR][1000 genomes]
rs221923	0.80[AMR][1000 genomes]
rs221927	0.81[AMR][1000 genomes]
rs2240533	0.91[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap]
rs2526850	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs2526851	0.86[AMR][1000 genomes]
rs2526857	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs2526858	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs2526868	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs2526877	0.82[ASW][hapmap]
rs2810096	0.84[AMR][1000 genomes]
rs2810097	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs2810098	0.82[ASW][hapmap]
rs2810099	0.94[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.84[AMR][1000 genomes]
rs2810104	0.93[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs2810105	0.82[AMR][1000 genomes]
rs2810114	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs3814871	0.82[ASW][hapmap]
rs3829954	0.87[AMR][1000 genomes]
rs56043821	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56268907	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56306703	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58815178	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59699904	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61990379	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs61990380	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61990387	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61992065	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61992087	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8007026	0.82[ASW][hapmap];0.80[TSI][hapmap]
rs8010063	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8013146	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8014273	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8181986	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs917065	0.82[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041980	chr14:71196358-71767339	Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv542125	chr14:71196358-71767339	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1035416	chr14:71212882-71623271	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv542126	chr14:71212882-71623271	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv1037839	chr14:71263886-71625114	Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv542127	chr14:71263886-71625114	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv1038007	chr14:71269747-71667680	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv565043	chr14:71395604-71625112	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv1036929	chr14:71469148-71683412	Strong transcription Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv1044090	chr14:71496198-71780026	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs17093738	PCNX	cis	normal skin	skin_eQTL
rs17093738	ZFYVE1	cis	cerebellum	SCAN
rs17093738	PCNX	cis	lymphoblastoid	seeQTL
rs17093738	PCNX	cis	parietal	SCAN
rs17093738	PCNX	cis	cerebellum	SCAN
rs17093738	PCNX	cis	Artery Tibial	GTEx
rs17093738	PCNX	cis	Thyroid	GTEx
rs17093738	PCNX	cis	Artery Aorta	GTEx
rs17093738	PCNX	cis	Nerve Tibial	GTEx

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71552000-71588400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr14:71575800-71588200	Weak transcription	Aorta	Aorta
3	chr14:71575800-71589800	Weak transcription	Fetal Brain Female	brain
4	chr14:71576400-71590400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr14:71576800-71588200	Weak transcription	Spleen	Spleen
6	chr14:71576800-71597000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr14:71577000-71586800	Weak transcription	Fetal Muscle Trunk	muscle
8	chr14:71577000-71588200	Weak transcription	Lung	lung
9	chr14:71577000-71590800	Weak transcription	Brain Germinal Matrix	brain
10	chr14:71577600-71587400	Weak transcription	Primary T cells from cord blood	blood
11	chr14:71577600-71589600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr14:71577800-71587400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr14:71578400-71587400	Weak transcription	A549	lung
14	chr14:71578400-71587800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr14:71578600-71586800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr14:71578600-71588600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr14:71581200-71586800	Enhancers	HepG2	liver
18	chr14:71581200-71588800	Enhancers	Duodenum Mucosa	Duodenum
19	chr14:71581200-71588800	Enhancers	Fetal Intestine Large	intestine
20	chr14:71581600-71587400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr14:71581600-71590200	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr14:71581800-71586800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr14:71582200-71597400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr14:71582400-71597000	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr14:71582600-71597000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr14:71582800-71587600	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr14:71582800-71597200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr14:71583000-71586800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr14:71583000-71587000	Weak transcription	Primary hematopoietic stem cells	blood
30	chr14:71583400-71588000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr14:71583600-71588200	Weak transcription	Left Ventricle	heart
32	chr14:71583800-71590400	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr14:71584200-71587800	Enhancers	Fetal Intestine Small	intestine
34	chr14:71584200-71588200	Weak transcription	Primary B cells from cord blood	blood
35	chr14:71584400-71586800	Enhancers	NH-A	brain
36	chr14:71584400-71587000	Enhancers	NHDF-Ad	bronchial
37	chr14:71584400-71587200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr14:71584400-71587400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr14:71584800-71588800	Enhancers	Small Intestine	intestine
40	chr14:71585200-71587000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr14:71585200-71587400	Enhancers	Osteobl	bone
42	chr14:71585200-71588200	Enhancers	Rectal Mucosa Donor 29	rectum
43	chr14:71585400-71587200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr14:71585400-71590200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr14:71585400-71593000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr14:71585600-71588000	Weak transcription	Fetal Stomach	stomach
47	chr14:71585800-71586800	Enhancers	NHEK	skin
48	chr14:71585800-71587800	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr14:71585800-71588200	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr14:71585800-71596800	Weak transcription	Primary neutrophils fromperipheralblood	blood

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