Variant report

Variant	rs221906
Chromosome Location	chr14:71597393-71597394
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10132789	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10132984	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10140225	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10140917	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10145824	0.82[AMR][1000 genomes]
rs10147068	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10148324	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10150408	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs116016	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12893492	0.87[EUR][1000 genomes]
rs12896829	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1468470	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1558097	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs190096	0.82[ASN][1000 genomes]
rs2097975	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs221888	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs221889	0.84[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs221891	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs221892	0.84[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs221893	0.90[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs221894	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs221896	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs221898	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.80[LWK][hapmap];0.88[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs221900	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs221901	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs221904	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs221908	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs221910	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs221913	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs221914	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs221915	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs221916	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs221917	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs221918	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs221919	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs221924	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs221925	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs221926	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2240531	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2251394	0.85[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes]
rs2286311	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2332506	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2332507	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2526847	0.85[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap]
rs2526856	0.84[ASW][hapmap];0.88[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap]
rs2526859	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2877708	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2877714	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34542576	0.82[ASN][1000 genomes]
rs3784067	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4132848	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4147077	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4366661	0.92[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes]
rs4467005	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4531677	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4899382	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs58938327	0.80[AMR][1000 genomes]
rs6573994	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7143595	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs7144986	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7145285	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7147862	0.81[AMR][1000 genomes]
rs7152845	0.85[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.89[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7154395	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7154437	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs7155247	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs7156009	0.85[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8005160	0.92[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap]
rs8006046	0.85[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8007425	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8008111	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8020480	0.85[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8021824	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9323556	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9323557	0.85[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9806042	0.93[EUR][1000 genomes];0.86[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs221906	PCNX	cis	parietal	SCAN
rs221906	PCNX	cis	Nerve Tibial	GTEx
rs221906	PCNX	cis	cerebellum	SCAN
rs221906	PCNX	cis	Skin Sun Exposed Lower leg	GTEx
rs221906	PCNX	cis	Artery Tibial	GTEx
rs221906	PCNX	cis	Thyroid	GTEx
rs221906	PCNX	cis	Artery Aorta	GTEx
rs221906	ZFYVE1	cis	cerebellum	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71582200-71597400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr14:71588800-71597400	Weak transcription	Adipose Nuclei	Adipose
3	chr14:71592800-71597400	Weak transcription	Duodenum Mucosa	Duodenum
4	chr14:71595600-71598400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr14:71595800-71597600	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr14:71596600-71597400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr14:71596600-71597400	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr14:71596600-71597600	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr14:71596600-71597800	Enhancers	Placenta	Placenta
10	chr14:71596600-71598200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr14:71596800-71597400	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr14:71596800-71597400	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr14:71596800-71597400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr14:71596800-71597400	Flanking Active TSS	Hela-S3	cervix
15	chr14:71596800-71597400	Enhancers	HUVEC	blood vessel
16	chr14:71596800-71597600	Enhancers	H1 Cell Line	embryonic stem cell
17	chr14:71596800-71597600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr14:71596800-71597800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
19	chr14:71596800-71597800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr14:71596800-71597800	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr14:71596800-71597800	Enhancers	Left Ventricle	heart
22	chr14:71596800-71597800	Flanking Active TSS	K562	blood
23	chr14:71596800-71598200	Enhancers	NHEK	skin
24	chr14:71596800-71598400	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr14:71596800-71598400	Enhancers	NHLF	lung
26	chr14:71597000-71597400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr14:71597000-71597400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr14:71597000-71597400	Enhancers	Muscle Satellite Cultured Cells	--
29	chr14:71597000-71597600	Enhancers	Fetal Intestine Small	intestine
30	chr14:71597000-71597800	Enhancers	Primary hematopoietic stem cells	blood
31	chr14:71597000-71597800	Enhancers	Placenta Amnion	Placenta Amnion
32	chr14:71597000-71597800	Enhancers	Spleen	Spleen
33	chr14:71597000-71597800	Flanking Active TSS	NH-A	brain
34	chr14:71597000-71597800	Enhancers	NHDF-Ad	bronchial
35	chr14:71597000-71598000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr14:71597000-71598000	Enhancers	HMEC	breast
37	chr14:71597000-71598200	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr14:71597000-71598200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr14:71597000-71598200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr14:71597000-71598200	Enhancers	Fetal Heart	heart
41	chr14:71597000-71598400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr14:71597200-71597400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr14:71597200-71597400	Flanking Active TSS	Osteobl	bone
44	chr14:71597200-71597600	Enhancers	H9 Cell Line	embryonic stem cell
45	chr14:71597200-71597600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr14:71597200-71597600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr14:71597200-71597600	Active TSS	Monocytes-CD14+_RO01746	blood
48	chr14:71597200-71597800	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr14:71597200-71597800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr14:71597200-71597800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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