Variant report

Variant	rs36555
Chromosome Location	chr14:71364561-71364562
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:71362265..71365941-chr14:71372682..71376130,7	MCF-7	breast:
2	chr14:71359505..71362289-chr14:71363900..71365887,4	MCF-7	breast:
3	chr14:71362952..71365427-chr14:71368027..71370762,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100731	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs12100737	0.82[ASW][hapmap];0.88[TSI][hapmap]
rs17108804	0.81[ASW][hapmap];0.88[TSI][hapmap]
rs17108808	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17108862	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2010061	0.80[AMR][1000 genomes]
rs2158996	0.82[AMR][1000 genomes]
rs2158997	0.82[ASW][hapmap];0.88[TSI][hapmap]
rs2240533	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.83[TSI][hapmap]
rs2526850	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2526851	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2526854	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2526857	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2526858	0.94[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2526868	0.94[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.91[YRI][hapmap]
rs2526872	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2526876	0.80[AMR][1000 genomes]
rs2526877	0.82[ASW][hapmap];0.87[TSI][hapmap]
rs2526878	0.80[AMR][1000 genomes]
rs2526879	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2810073	0.82[ASW][hapmap];0.88[TSI][hapmap]
rs2810075	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2810096	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2810097	0.94[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.91[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2810098	0.82[ASW][hapmap];0.88[TSI][hapmap]
rs2810099	0.94[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2810104	0.93[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2810105	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2810114	0.94[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs36559	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36567	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3814871	0.82[ASW][hapmap];0.88[TSI][hapmap]
rs3829954	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56306703	0.82[AMR][1000 genomes]
rs61990379	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61990380	0.80[EUR][1000 genomes]
rs61990387	0.82[AMR][1000 genomes]
rs8007026	0.82[ASW][hapmap];0.90[TSI][hapmap]
rs8010063	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[AMR][1000 genomes]
rs8014273	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[AMR][1000 genomes]
rs917065	0.82[ASW][hapmap];0.88[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039460	chr14:71176898-71371125	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	nsv1049741	chr14:71233043-71462509	Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	nsv1039769	chr14:71310954-71525720	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv542128	chr14:71310954-71525720	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv1053303	chr14:71316325-71402971	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs36555	PCNX	cis	Artery Aorta	GTEx
rs36555	PCNX	cis	parietal	SCAN
rs36555	PCNX	Cis_1M	lymphoblastoid	RTeQTL
rs36555	PCNX	cis	Thyroid	GTEx
rs36555	PCNX	cis	lymphoblastoid	seeQTL
rs36555	PCNX	cis	Nerve Tibial	GTEx
rs36555	ZFYVE1	cis	cerebellum	SCAN
rs36555	PCNX	cis	Artery Tibial	GTEx
rs36555	PCNX	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71350600-71373000	Weak transcription	Spleen	Spleen
2	chr14:71351800-71365200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr14:71353200-71365200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr14:71355000-71371600	Weak transcription	Placenta	Placenta
5	chr14:71361200-71366800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr14:71361800-71373400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr14:71362200-71368200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr14:71362200-71370800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr14:71362200-71371600	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr14:71362400-71371600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr14:71363400-71365400	Enhancers	Fetal Brain Male	brain
12	chr14:71363400-71366200	Enhancers	Colon Smooth Muscle	Colon
13	chr14:71363600-71364600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr14:71363600-71365400	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr14:71363800-71364600	Enhancers	Ovary	ovary
16	chr14:71363800-71365400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr14:71363800-71365400	Enhancers	HSMMtube	muscle
18	chr14:71363800-71365600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr14:71363800-71365600	Enhancers	Fetal Stomach	stomach
20	chr14:71363800-71366000	Enhancers	Rectal Smooth Muscle	rectum
21	chr14:71363800-71366000	Enhancers	NHLF	lung
22	chr14:71363800-71366000	Enhancers	Osteobl	bone
23	chr14:71363800-71366200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr14:71363800-71368800	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr14:71364000-71364800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr14:71364000-71365200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr14:71364000-71365400	Enhancers	Muscle Satellite Cultured Cells	--
28	chr14:71364000-71365400	Enhancers	Fetal Lung	lung
29	chr14:71364000-71365400	Enhancers	Fetal Muscle Leg	muscle
30	chr14:71364000-71365400	Enhancers	Hela-S3	cervix
31	chr14:71364000-71365800	Enhancers	NH-A	brain
32	chr14:71364000-71366000	Enhancers	Adipose Nuclei	Adipose
33	chr14:71364000-71366400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr14:71364000-71373800	Weak transcription	Small Intestine	intestine
35	chr14:71364200-71365200	Weak transcription	Right Atrium	heart
36	chr14:71364200-71365200	Weak transcription	HMEC	breast
37	chr14:71364200-71365600	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr14:71364200-71368200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr14:71364200-71368200	Weak transcription	Aorta	Aorta
40	chr14:71364200-71373000	Weak transcription	NHEK	skin
41	chr14:71364200-71373600	Weak transcription	Lung	lung
42	chr14:71364400-71364600	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr14:71364400-71364600	Enhancers	HSMM	muscle
44	chr14:71364400-71365200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr14:71364400-71365200	Weak transcription	Stomach Smooth Muscle	stomach
46	chr14:71364400-71365800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr14:71364400-71366000	Enhancers	NHDF-Ad	bronchial

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