Variant report

Variant	rs2810082
Chromosome Location	chr14:71356032-71356033
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	chr14:71355468..71357237-chr14:71359840..71362416,2	MCF-7	breast:
2	chr14:71355596..71357238-chr14:71373559..71375113,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100731	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10140225	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs10140917	0.81[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap]
rs11623266	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1468470	0.81[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap]
rs1978164	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2010713	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs2240341	0.80[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs2240531	0.80[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap]
rs2251394	0.80[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs2286311	0.81[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap]
rs2526847	0.80[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs2526856	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs2526859	0.92[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs2526867	1.00[CHB][hapmap]
rs2526873	0.83[AMR][1000 genomes]
rs2526875	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.80[EUR][1000 genomes]
rs2526880	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2526883	0.90[ASN][1000 genomes]
rs2526884	0.89[ASN][1000 genomes]
rs2526887	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2810074	0.83[AMR][1000 genomes]
rs2810077	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2810078	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2810079	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2810081	0.89[CEU][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2810113	1.00[CHB][hapmap]
rs3784067	0.81[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs4132848	0.81[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap]
rs4366661	0.80[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs4467005	0.80[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap]
rs4531677	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs6573994	0.81[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap]
rs7143595	0.81[CEU][hapmap];0.92[CHB][hapmap]
rs714421	0.80[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7144986	0.81[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap]
rs7152845	0.80[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs7154437	0.80[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap]
rs7156009	0.80[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs8005160	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs8006046	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs8007425	0.81[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap]
rs8008111	0.81[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap]
rs8020480	0.80[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs8021824	0.81[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap]
rs917067	1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs9323556	0.81[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap]
rs9323557	0.80[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2810082	PCNX	cis	Artery Aorta	GTEx
rs2810082	PCNX	cis	Nerve Tibial	GTEx
rs2810082	PCNX	cis	Skin Sun Exposed Lower leg	GTEx
rs2810082	PCNX	Cis_1M	lymphoblastoid	RTeQTL
rs2810082	PCNX	cis	Thyroid	GTEx
rs2810082	PCNX	cis	Artery Tibial	GTEx

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71349800-71356200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
2	chr14:71350000-71356200	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr14:71350600-71356600	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr14:71350600-71373000	Weak transcription	Spleen	Spleen
5	chr14:71351200-71357400	Enhancers	Fetal Thymus	thymus
6	chr14:71351800-71361000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr14:71351800-71365200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr14:71353200-71365200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr14:71353600-71356600	Enhancers	NHLF	lung
10	chr14:71353600-71356800	Enhancers	HMEC	breast
11	chr14:71353600-71360800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr14:71353800-71356600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr14:71353800-71357400	Enhancers	Primary T cells fromperipheralblood	blood
14	chr14:71354000-71356400	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr14:71354000-71360000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr14:71354200-71356600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr14:71354200-71356600	Enhancers	HSMMtube	muscle
18	chr14:71354200-71356800	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr14:71354400-71356200	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr14:71354400-71356200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr14:71354400-71356200	Enhancers	HSMM	muscle
22	chr14:71354400-71356600	Enhancers	Primary hematopoietic stem cells	blood
23	chr14:71354400-71359600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr14:71354400-71359800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr14:71354600-71356200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr14:71354600-71356200	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr14:71354600-71356400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr14:71354600-71356600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr14:71354600-71357400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr14:71354600-71358400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr14:71354600-71360000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr14:71354800-71356200	Enhancers	Dnd41	blood
33	chr14:71354800-71356600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr14:71354800-71356600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr14:71354800-71363800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr14:71355000-71356400	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr14:71355000-71356600	Enhancers	Osteobl	bone
38	chr14:71355000-71357800	Enhancers	GM12878-XiMat	blood
39	chr14:71355000-71371600	Weak transcription	Placenta	Placenta
40	chr14:71355600-71356400	Enhancers	Muscle Satellite Cultured Cells	--
41	chr14:71355600-71356600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr14:71355600-71357600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr14:71355600-71361000	Weak transcription	Small Intestine	intestine
44	chr14:71355600-71361200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr14:71355800-71356400	Enhancers	NH-A	brain
46	chr14:71355800-71356600	Enhancers	NHEK	skin
47	chr14:71355800-71359200	Weak transcription	Primary T cells from cord blood	blood
48	chr14:71355800-71361400	Weak transcription	Rectal Smooth Muscle	rectum
49	chr14:71356000-71356600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
50	chr14:71356000-71356600	Enhancers	NHDF-Ad	bronchial

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