Variant report

Variant	rs12893492
Chromosome Location	chr14:71506775-71506776
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10132789	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10132984	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10140225	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10140917	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10145824	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10147068	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10148324	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10150408	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs116016	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11623266	0.81[EUR][1000 genomes]
rs12896829	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1468470	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1558097	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2010713	0.80[EUR][1000 genomes]
rs2097975	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs221904	0.87[EUR][1000 genomes]
rs221906	0.87[EUR][1000 genomes]
rs221908	0.86[EUR][1000 genomes]
rs221910	0.80[EUR][1000 genomes]
rs221913	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs221914	0.85[EUR][1000 genomes]
rs221915	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs221916	0.88[EUR][1000 genomes]
rs221917	0.88[EUR][1000 genomes]
rs221918	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs221919	0.87[EUR][1000 genomes]
rs221924	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs221925	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs221926	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2240531	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2251394	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2286311	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2332506	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2332507	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2526847	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2526848	0.81[EUR][1000 genomes]
rs2526856	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2526859	0.83[EUR][1000 genomes]
rs2526864	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2526871	0.83[EUR][1000 genomes]
rs2526873	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2526875	0.80[EUR][1000 genomes]
rs2526880	0.82[EUR][1000 genomes]
rs2810072	0.80[AFR][1000 genomes]
rs2810074	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2810101	0.87[EUR][1000 genomes]
rs2810109	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2810111	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2810118	0.83[EUR][1000 genomes]
rs2877708	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2877714	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3784067	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4132848	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4147077	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4366661	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4467005	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4531677	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs58938327	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6573994	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7144986	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7145285	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7147862	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7150037	0.82[EUR][1000 genomes]
rs7152845	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7154395	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7154437	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7156009	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7160958	0.86[EUR][1000 genomes]
rs8004452	0.84[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs8006046	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8007425	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8008111	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8020480	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8021824	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9323556	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9323557	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9806042	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][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	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	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
9	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
10	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
11	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
12	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
rs12893492	PCNX	cis	Artery Aorta	GTEx
rs12893492	PCNX	Cis_1M	lymphoblastoid	RTeQTL
rs12893492	PCNX	cis	Thyroid	GTEx
rs12893492	PCNX	cis	Artery Tibial	GTEx
rs12893492	PCNX	cis	Skin Sun Exposed Lower leg	GTEx
rs12893492	PCNX	cis	Nerve Tibial	GTEx

Chromatin state (count:120 , 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	chr14:71445200-71510800	Weak transcription	Colonic Mucosa	Colon
3	chr14:71495800-71546200	Weak transcription	Stomach Mucosa	stomach
4	chr14:71497000-71554200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr14:71498600-71510800	Weak transcription	Esophagus	oesophagus
6	chr14:71498800-71510800	Weak transcription	NHLF	lung
7	chr14:71499600-71540800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr14:71501400-71507400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr14:71502000-71513600	Weak transcription	HepG2	liver
10	chr14:71502200-71511000	Weak transcription	HMEC	breast
11	chr14:71503000-71526400	Weak transcription	Gastric	stomach
12	chr14:71503400-71510800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr14:71503400-71510800	Weak transcription	Pancreas	Pancrea
14	chr14:71503400-71511000	Weak transcription	Small Intestine	intestine
15	chr14:71503400-71524400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr14:71503400-71526600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr14:71503400-71527200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr14:71503600-71507200	Weak transcription	Brain Anterior Caudate	brain
19	chr14:71503600-71507400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr14:71503600-71507400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr14:71503600-71508800	Weak transcription	Brain Angular Gyrus	brain
22	chr14:71503600-71509000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr14:71503600-71510600	Weak transcription	Brain Hippocampus Middle	brain
24	chr14:71503600-71510600	Weak transcription	Thymus	Thymus
25	chr14:71503600-71510600	Weak transcription	Hela-S3	cervix
26	chr14:71503600-71510800	Weak transcription	NHEK	skin
27	chr14:71503600-71519400	Weak transcription	Colon Smooth Muscle	Colon
28	chr14:71505800-71507600	ZNF genes & repeats	Primary B cells from cord blood	blood
29	chr14:71505800-71509000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr14:71505800-71511400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
31	chr14:71506000-71506800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr14:71506000-71506800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr14:71506000-71506800	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr14:71506000-71506800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr14:71506000-71506800	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
36	chr14:71506000-71506800	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
37	chr14:71506000-71506800	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
38	chr14:71506000-71506800	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr14:71506000-71506800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr14:71506000-71506800	ZNF genes & repeats	Aorta	Aorta
41	chr14:71506000-71506800	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
42	chr14:71506000-71506800	ZNF genes & repeats	Fetal Brain Male	brain
43	chr14:71506000-71506800	ZNF genes & repeats	Fetal Brain Female	brain
44	chr14:71506000-71506800	ZNF genes & repeats	Fetal Intestine Small	intestine
45	chr14:71506000-71506800	ZNF genes & repeats	Fetal Muscle Trunk	muscle
46	chr14:71506000-71506800	ZNF genes & repeats	Placenta	Placenta
47	chr14:71506000-71506800	Strong transcription	Fetal Stomach	stomach
48	chr14:71506000-71506800	Strong transcription	Fetal Thymus	thymus
49	chr14:71506000-71506800	ZNF genes & repeats	Lung	lung
50	chr14:71506000-71506800	ZNF genes & repeats	Spleen	Spleen

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