Variant report

Variant	rs116016
Chromosome Location	chr14:71577480-71577481
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:71576318..71579821-chr14:71580472..71584172,4	MCF-7	breast:
2	chr14:71576010..71578175-chr14:71578987..71581734,2	K562	blood:

Extended variants
information (count: 90 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10132789	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10132984	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10140225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10140917	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10145824	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10147068	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10148324	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10150408	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12893492	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12896829	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1468470	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1558097	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2097975	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs221888	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs221889	0.93[CEU][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs221891	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs221892	0.93[CEU][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs221893	0.81[CEU][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs221894	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs221896	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs221898	0.92[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs221900	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs221901	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs221904	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs221906	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs221908	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs221910	0.89[EUR][1000 genomes]
rs221913	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs221914	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs221915	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs221916	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs221917	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs221918	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs221919	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs221924	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs221925	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs221926	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2240531	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2251394	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2286311	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2332506	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2332507	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2526847	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs2526856	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs2526859	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2526867	0.83[CHB][hapmap]
rs2526875	0.89[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs2810101	0.81[EUR][1000 genomes]
rs2810109	0.82[AMR][1000 genomes]
rs2810113	0.84[CHB][hapmap]
rs2877708	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2877714	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34542576	0.87[ASN][1000 genomes]
rs3784067	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4132848	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4147077	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4366661	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4467005	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4531677	0.89[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs4899382	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs6573994	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7143595	1.00[CEU][hapmap];0.92[CHB][hapmap]
rs7144986	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7145285	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7147862	0.83[AMR][1000 genomes]
rs7152845	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7154395	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7154437	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7155247	0.94[JPT][hapmap]
rs7156009	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7160958	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs8005160	1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap]
rs8006046	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8007425	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8008111	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8020480	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8021824	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9323556	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9323557	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9806042	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]

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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs116016	PCNX	cis	Artery Aorta	GTEx
rs116016	PCNX	cis	Thyroid	GTEx
rs116016	PCNX	cis	Nerve Tibial	GTEx
rs116016	PCNX	Cis_1M	lymphoblastoid	RTeQTL
rs116016	PCNX	cis	Artery Tibial	GTEx
rs116016	PCNX	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71538800-71584800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr14:71544800-71581400	Weak transcription	Small Intestine	intestine
3	chr14:71552000-71588400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr14:71556000-71582200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr14:71556400-71583000	Weak transcription	Brain Substantia Nigra	brain
6	chr14:71557200-71582000	Weak transcription	HUVEC	blood vessel
7	chr14:71559800-71584000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr14:71564000-71583600	Weak transcription	Fetal Brain Male	brain
9	chr14:71566600-71582200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr14:71566600-71582600	Strong transcription	Primary T helper cells PMA-I stimulated	--
11	chr14:71566800-71582400	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr14:71566800-71583400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr14:71566800-71585800	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr14:71567200-71578800	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr14:71567200-71581600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr14:71567200-71583800	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr14:71567400-71581600	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr14:71567600-71577800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr14:71567600-71578800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr14:71567600-71582600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr14:71568000-71577800	Strong transcription	Primary B cells from peripheral blood	blood
22	chr14:71568400-71578800	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr14:71568600-71577800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr14:71568600-71578400	Strong transcription	Liver	Liver
25	chr14:71568600-71578600	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr14:71568600-71578800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr14:71568800-71577600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr14:71568800-71577600	Strong transcription	Fetal Intestine Large	intestine
29	chr14:71568800-71577600	Strong transcription	GM12878-XiMat	blood
30	chr14:71568800-71577800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr14:71568800-71578200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr14:71568800-71578200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr14:71568800-71578800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr14:71569600-71577600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr14:71570000-71577600	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr14:71570000-71578600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr14:71570400-71577600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr14:71570600-71579800	Weak transcription	Brain Angular Gyrus	brain
39	chr14:71570600-71581800	Weak transcription	Psoas Muscle	Psoas
40	chr14:71571400-71578800	Strong transcription	Adipose Nuclei	Adipose
41	chr14:71571600-71578400	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr14:71571800-71578800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr14:71572200-71577600	Strong transcription	NH-A	brain
44	chr14:71572200-71578000	Weak transcription	A549	lung
45	chr14:71572200-71578200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr14:71572200-71578200	Strong transcription	Hela-S3	cervix
47	chr14:71572200-71585400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr14:71572400-71578400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr14:71572400-71579000	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr14:71572400-71581400	Weak transcription	Stomach Mucosa	stomach

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