Variant report

Variant	rs917067
Chromosome Location	chr14:71371904-71371905
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr14:71371711-71373446	MCF10A-Er-Src	breast:	n/a	n/a
2	MAX	chr14:71371638-71371909	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
PCNX	TF binding region

Extended variants
information (count: 87 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10132789	0.83[EUR][1000 genomes]
rs10132984	0.84[EUR][1000 genomes]
rs10140225	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs10140917	0.89[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs10145824	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10148324	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10150408	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs11623266	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12896829	0.88[EUR][1000 genomes]
rs1468470	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs1558097	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs1978164	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2010713	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2097975	0.83[EUR][1000 genomes]
rs2240341	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2240531	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2251394	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2286311	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2332506	0.87[EUR][1000 genomes]
rs2526847	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2526848	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2526856	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2526859	0.86[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2526864	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2526867	1.00[CHB][hapmap]
rs2526871	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2526873	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2526875	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2526880	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2526881	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2526883	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2526884	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2526887	0.87[ASN][1000 genomes]
rs2810072	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2810074	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2810077	1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2810078	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2810079	1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2810081	0.84[ASN][1000 genomes]
rs2810082	1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs2810101	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2810109	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2810111	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2810113	1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2810118	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2877708	0.83[EUR][1000 genomes]
rs2877714	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs3784067	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs4132848	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4147077	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4366661	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4467005	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs4531677	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58938327	0.88[EUR][1000 genomes]
rs6573994	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs7143595	0.89[CEU][hapmap];0.92[CHB][hapmap]
rs714421	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7144986	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs7145285	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs7147862	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7150037	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7151145	0.87[ASN][1000 genomes]
rs7152845	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7154437	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7156009	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs7156673	0.80[ASN][1000 genomes]
rs7160958	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8004452	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8005160	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs8006046	0.89[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs8007425	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs8008111	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs8020480	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs8021824	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs9323556	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs9323557	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
6	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
7	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
8	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
9	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
10	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
11	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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs917067	PCNX	cis	Esophagus Muscularis	GTEx
rs917067	PCNX	cis	Thyroid	GTEx
rs917067	PCNX	cis	Adipose Subcutaneous	GTEx
rs917067	PCNX	cis	Artery Tibial	GTEx
rs917067	PCNX	cis	Skin Sun Exposed Lower leg	GTEx
rs917067	PCNX	Cis_1M	lymphoblastoid	RTeQTL
rs917067	PCNX	cis	Nerve Tibial	GTEx
rs917067	PCNX	cis	Artery Aorta	GTEx

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71350600-71373000	Weak transcription	Spleen	Spleen
2	chr14:71361800-71373400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr14:71364000-71373800	Weak transcription	Small Intestine	intestine
4	chr14:71364200-71373000	Weak transcription	NHEK	skin
5	chr14:71364200-71373600	Weak transcription	Lung	lung
6	chr14:71365400-71373400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr14:71368000-71372200	Weak transcription	Gastric	stomach
8	chr14:71368200-71373000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr14:71368600-71373000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr14:71368600-71373200	Weak transcription	GM12878-XiMat	blood
11	chr14:71368600-71373200	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr14:71368600-71373400	Weak transcription	NH-A	brain
13	chr14:71368600-71373600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr14:71368800-71373000	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr14:71368800-71373600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr14:71369200-71373200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr14:71370200-71372000	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr14:71370400-71373000	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr14:71370600-71373000	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr14:71370600-71373400	Enhancers	Fetal Muscle Leg	muscle
21	chr14:71370600-71373400	Enhancers	Fetal Stomach	stomach
22	chr14:71370800-71372000	Enhancers	NHDF-Ad	bronchial
23	chr14:71370800-71372200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr14:71370800-71372400	Enhancers	Left Ventricle	heart
25	chr14:71370800-71372800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr14:71370800-71373200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr14:71370800-71373400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr14:71370800-71373600	Enhancers	Fetal Lung	lung
29	chr14:71371000-71372000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr14:71371000-71372000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr14:71371000-71372000	Enhancers	NHLF	lung
32	chr14:71371000-71372400	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr14:71371000-71373000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr14:71371000-71373000	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr14:71371000-71373400	Enhancers	Ovary	ovary
36	chr14:71371000-71373600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr14:71371200-71372000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
38	chr14:71371200-71372000	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr14:71371200-71372400	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr14:71371200-71372400	Enhancers	Fetal Kidney	kidney
41	chr14:71371200-71372800	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr14:71371200-71373000	Enhancers	Rectal Smooth Muscle	rectum
43	chr14:71371200-71373200	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr14:71371200-71373400	Enhancers	Muscle Satellite Cultured Cells	--
45	chr14:71371200-71373600	Weak transcription	Colonic Mucosa	Colon
46	chr14:71371200-71373600	Enhancers	HSMM	muscle
47	chr14:71371200-71374200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr14:71371400-71373000	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr14:71371400-71373400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr14:71371400-71373400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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