Variant report

Variant	rs17108822
Chromosome Location	chr14:71445906-71445907
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1018977	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12100737	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12101246	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12883437	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12892739	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12896370	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12897533	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17108804	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17108808	0.81[AMR][1000 genomes]
rs17108877	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17108925	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17108967	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1859468	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2010061	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2097866	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2158997	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2189806	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2189807	0.85[EUR][1000 genomes]
rs221899	0.82[AMR][1000 genomes]
rs221902	0.82[AMR][1000 genomes]
rs221909	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs221912	0.85[AMR][1000 genomes]
rs221920	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs221921	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs221922	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs221923	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs221927	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2286310	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2332477	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2526846	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2526852	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2526855	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2526860	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2526862	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2526874	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2526876	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2526877	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2526878	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2526882	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2526886	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2526890	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2810071	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2810073	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2810098	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2810100	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2810107	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2810115	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2810116	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2810117	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28374308	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34049963	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34257131	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34368938	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34488204	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34731365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34763296	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35631530	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3814869	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3814871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3829954	0.81[AMR][1000 genomes]
rs4048474	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4132849	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4391999	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4426283	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56021283	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58133478	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58984901	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61990419	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67981189	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7145484	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7146591	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7146932	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7153237	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7157250	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8003103	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8003227	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8007026	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8012728	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8016506	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8022768	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs917065	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs989501	0.83[AMR][1000 genomes];0.86[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	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17108822	PCNX	cis	Skin Sun Exposed Lower leg	GTEx
rs17108822	PCNX	cis	Artery Tibial	GTEx
rs17108822	PCNX	cis	Artery Aorta	GTEx
rs17108822	PCNX	Cis_1M	lymphoblastoid	RTeQTL
rs17108822	PCNX	cis	Thyroid	GTEx
rs17108822	PCNX	cis	Nerve Tibial	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71426000-71508800	Weak transcription	Psoas Muscle	Psoas
2	chr14:71428000-71446200	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr14:71432000-71446800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr14:71433200-71455200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr14:71437200-71485600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr14:71438600-71502800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr14:71439200-71454800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr14:71439200-71478000	Weak transcription	Colon Smooth Muscle	Colon
9	chr14:71439400-71446400	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr14:71439600-71446000	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr14:71439600-71502800	Weak transcription	Small Intestine	intestine
12	chr14:71440000-71446000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr14:71440200-71446400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr14:71441200-71447000	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr14:71442600-71446000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr14:71442600-71446000	Strong transcription	Liver	Liver
17	chr14:71442800-71446200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr14:71443400-71446200	Strong transcription	HMEC	breast
19	chr14:71443400-71446400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr14:71443400-71446800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr14:71443600-71446200	Strong transcription	NH-A	brain
22	chr14:71443600-71446400	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr14:71443600-71446400	Strong transcription	HUVEC	blood vessel
24	chr14:71443800-71446200	Strong transcription	Fetal Lung	lung
25	chr14:71444600-71446600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr14:71444800-71446400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
27	chr14:71445000-71446400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr14:71445000-71449800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr14:71445000-71461800	Weak transcription	A549	lung
30	chr14:71445200-71446000	Weak transcription	Primary hematopoietic stem cells	blood
31	chr14:71445200-71446200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr14:71445200-71446400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr14:71445200-71447000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr14:71445200-71447200	Weak transcription	HSMM	muscle
35	chr14:71445200-71447400	Weak transcription	NHLF	lung
36	chr14:71445200-71453800	Weak transcription	Stomach Mucosa	stomach
37	chr14:71445200-71462400	Weak transcription	Esophagus	oesophagus
38	chr14:71445200-71462400	Weak transcription	Gastric	stomach
39	chr14:71445200-71462400	Weak transcription	Lung	lung
40	chr14:71445200-71470800	Weak transcription	GM12878-XiMat	blood
41	chr14:71445200-71471000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr14:71445200-71496200	Weak transcription	Fetal Brain Male	brain
43	chr14:71445200-71497800	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr14:71445200-71502800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr14:71445200-71510800	Weak transcription	Colonic Mucosa	Colon
46	chr14:71445400-71446000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr14:71445400-71446000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr14:71445400-71446000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr14:71445400-71446000	Weak transcription	Brain Anterior Caudate	brain
50	chr14:71445400-71446200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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