Variant report

Variant	rs989501
Chromosome Location	chr14:71361414-71361415
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:71355468..71357237-chr14:71359840..71362416,2	MCF-7	breast:
2	chr14:71359184..71361695-chr14:71373251..71375700,2	MCF-7	breast:
3	chr14:71359505..71362289-chr14:71363900..71365887,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100731	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1018977	0.81[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12100737	0.81[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12101246	0.80[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes]
rs12883437	0.84[EUR][1000 genomes]
rs12892739	0.94[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12896370	0.94[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes]
rs17108804	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17108822	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17108877	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17108925	0.81[AMR][1000 genomes]
rs1859468	0.81[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2010061	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2097866	0.87[AMR][1000 genomes]
rs2158997	0.81[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes]
rs2189806	0.81[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2189807	0.82[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2286310	0.81[AMR][1000 genomes]
rs2332477	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2526846	0.87[EUR][1000 genomes]
rs2526852	0.80[AMR][1000 genomes]
rs2526855	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2526860	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2526862	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2526867	0.84[JPT][hapmap]
rs2526874	0.81[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2526876	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2526877	0.88[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2526878	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2526882	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2526886	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2526890	0.86[EUR][1000 genomes]
rs2810071	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2810073	0.81[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2810098	0.81[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2810100	0.81[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2810107	0.87[EUR][1000 genomes]
rs2810113	0.85[JPT][hapmap]
rs2810115	0.81[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2810116	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2810117	0.83[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28374308	0.81[AMR][1000 genomes]
rs34049963	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34257131	0.81[AMR][1000 genomes]
rs34368938	0.81[AMR][1000 genomes]
rs34488204	0.81[AMR][1000 genomes]
rs34731365	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34763296	0.81[AMR][1000 genomes]
rs35631530	0.81[AMR][1000 genomes]
rs3814869	0.81[AMR][1000 genomes]
rs3814871	0.81[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4048474	0.94[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes]
rs4132849	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4391999	0.94[CHB][hapmap];0.85[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4426283	0.81[AMR][1000 genomes]
rs56021283	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58133478	0.81[AMR][1000 genomes]
rs58984901	0.81[AMR][1000 genomes]
rs61990419	0.80[AMR][1000 genomes]
rs7143595	0.81[JPT][hapmap]
rs7145484	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7146591	0.81[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes]
rs7146932	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7153237	0.81[AMR][1000 genomes]
rs7157250	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8003103	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8003227	0.81[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.80[AMR][1000 genomes]
rs8007026	0.94[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8012728	0.94[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8016506	0.81[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes]
rs8022768	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs917065	0.81[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]

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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs989501	PCNX	cis	lymphoblastoid	seeQTL
rs989501	PCNX	cis	Artery Aorta	GTEx
rs989501	PCNX	Cis_1M	lymphoblastoid	RTeQTL
rs989501	PCNX	cis	Artery Tibial	GTEx
rs989501	PCNX	cis	cerebellum	SCAN
rs989501	PCNX	cis	Skin Sun Exposed Lower leg	GTEx
rs989501	ZFYVE1	cis	cerebellum	SCAN
rs989501	PCNX	cis	Nerve Tibial	GTEx
rs989501	PCNX	cis	Adipose Subcutaneous	GTEx
rs989501	PCNX	cis	Thyroid	GTEx
rs989501	PCNX	cis	parietal	SCAN

Chromatin state (count:50 , 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	chr14:71354800-71363800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr14:71355000-71371600	Weak transcription	Placenta	Placenta
6	chr14:71356200-71361600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr14:71356400-71361600	Weak transcription	NH-A	brain
8	chr14:71356600-71363600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr14:71356600-71363800	Weak transcription	NHLF	lung
10	chr14:71356800-71363800	Weak transcription	HMEC	breast
11	chr14:71357400-71362200	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr14:71357400-71362600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr14:71357800-71363800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr14:71358600-71362000	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr14:71358600-71363800	Weak transcription	Right Atrium	heart
16	chr14:71358800-71363200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr14:71359000-71362200	Enhancers	Fetal Thymus	thymus
18	chr14:71359200-71362200	Enhancers	Primary T cells from cord blood	blood
19	chr14:71359200-71362200	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr14:71359400-71362000	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr14:71359400-71362200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr14:71359400-71362200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr14:71360000-71361800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr14:71360000-71362200	Enhancers	Primary T cells fromperipheralblood	blood
25	chr14:71360200-71362400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr14:71360800-71361600	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr14:71360800-71361600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
28	chr14:71360800-71361800	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr14:71360800-71362200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr14:71361000-71362000	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr14:71361000-71362200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr14:71361000-71362200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr14:71361000-71362600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr14:71361000-71362800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr14:71361200-71361600	Enhancers	GM12878-XiMat	blood
36	chr14:71361200-71361600	Flanking Active TSS	HepG2	liver
37	chr14:71361200-71361800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr14:71361200-71362000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr14:71361200-71363800	Weak transcription	Small Intestine	intestine
40	chr14:71361200-71366800	Weak transcription	Primary hematopoietic stem cells	blood
41	chr14:71361400-71361800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr14:71361400-71361800	Enhancers	NHDF-Ad	bronchial
43	chr14:71361400-71362000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr14:71361400-71362000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr14:71361400-71362000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr14:71361400-71362000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr14:71361400-71362000	Enhancers	Rectal Smooth Muscle	rectum
48	chr14:71361400-71362000	Enhancers	Stomach Smooth Muscle	stomach
49	chr14:71361400-71362000	Enhancers	Osteobl	bone
50	chr14:71361400-71362400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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