Variant report

Variant	rs17108967
Chromosome Location	chr14:71542168-71542169
allele	C/T
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	CEBPB	chr14:71541964-71542268	HepG2	liver:	n/a	chr14:71542124-71542137 chr14:71542124-71542135
2	CEBPB	chr14:71541965-71542254	A549	lung:	n/a	chr14:71542124-71542137 chr14:71542124-71542135
3	CEBPB	chr14:71542002-71542269	IMR90	lung:	n/a	chr14:71542124-71542137 chr14:71542124-71542135

Variant related genes	Relation type
PCNX	TF binding region

Extended variants
information (count: 91 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1018977	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12100737	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12101246	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12883437	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12892739	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12896370	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12897533	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17108804	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17108822	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17108877	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17108925	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1859468	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2010061	0.85[AMR][1000 genomes]
rs2097866	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2158997	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2189806	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs221899	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs221902	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs221903	0.87[ASN][1000 genomes]
rs221907	0.87[ASN][1000 genomes]
rs221909	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs221912	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs221920	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs221921	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs221922	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs221923	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs221927	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2286310	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2332477	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2526846	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2526852	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2526855	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2526860	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2526862	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2526874	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2526876	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2526877	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2526878	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2526882	0.82[AMR][1000 genomes]
rs2526886	0.82[AMR][1000 genomes]
rs2526890	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2810071	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2810073	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2810098	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2810100	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2810107	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2810115	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2810116	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2810117	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs28374308	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34049963	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34093157	0.83[EUR][1000 genomes]
rs34257131	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34368938	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34488204	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34731365	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34763296	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35631530	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3814869	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3814871	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4048474	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4132849	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4391999	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4426283	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56021283	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58133478	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58984901	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61990419	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67981189	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7145484	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7146591	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7146932	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7153237	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7157250	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8003103	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8003227	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8007026	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8012728	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8016506	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8022768	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs917065	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][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
rs17108967	PCNX	cis	Nerve Tibial	GTEx
rs17108967	PCNX	cis	Thyroid	GTEx
rs17108967	PCNX	cis	Artery Aorta	GTEx
rs17108967	PCNX	cis	Artery Tibial	GTEx
rs17108967	PCNX	cis	Skin Sun Exposed Lower leg	GTEx
rs17108967	PCNX	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71495800-71546200	Weak transcription	Stomach Mucosa	stomach
2	chr14:71497000-71554200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr14:71518200-71544000	Strong transcription	Primary T helper cells PMA-I stimulated	--
4	chr14:71528000-71543200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr14:71528600-71543200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr14:71529000-71543000	Weak transcription	Psoas Muscle	Psoas
7	chr14:71532400-71543000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr14:71533400-71543800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr14:71533600-71545000	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr14:71533800-71543000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr14:71533800-71545000	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr14:71533800-71546400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr14:71534000-71543200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr14:71534000-71544200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr14:71534400-71544000	Strong transcription	Liver	Liver
16	chr14:71534400-71546200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr14:71534600-71544000	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr14:71534600-71546400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr14:71535000-71546200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr14:71535200-71545800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr14:71535600-71543000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr14:71535600-71543800	Strong transcription	Primary B cells from peripheral blood	blood
23	chr14:71535600-71543800	Strong transcription	Fetal Muscle Trunk	muscle
24	chr14:71535600-71543800	Strong transcription	Fetal Muscle Leg	muscle
25	chr14:71535600-71544000	Strong transcription	Dnd41	blood
26	chr14:71535600-71544600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr14:71535600-71545000	Strong transcription	Duodenum Mucosa	Duodenum
28	chr14:71535600-71545200	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr14:71535600-71545400	Strong transcription	Fetal Intestine Large	intestine
30	chr14:71535600-71545800	Strong transcription	Left Ventricle	heart
31	chr14:71535800-71544000	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr14:71535800-71544000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr14:71535800-71544800	Strong transcription	Adipose Nuclei	Adipose
34	chr14:71535800-71546400	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr14:71536200-71544200	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr14:71536200-71545000	Strong transcription	Brain Anterior Caudate	brain
37	chr14:71536200-71545400	Strong transcription	Stomach Smooth Muscle	stomach
38	chr14:71536400-71543000	Strong transcription	GM12878-XiMat	blood
39	chr14:71536600-71544000	Weak transcription	Colonic Mucosa	Colon
40	chr14:71536800-71543000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr14:71537200-71543000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr14:71537200-71545000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr14:71537400-71542400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr14:71537400-71544800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr14:71537800-71544000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr14:71537800-71546400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr14:71538000-71544000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr14:71538000-71544000	Strong transcription	Fetal Lung	lung
49	chr14:71538000-71545800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr14:71538200-71543800	Strong transcription	Primary T helper cells fromperipheralblood	blood

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