Variant report

Variant	rs4147077
Chromosome Location	chr14:71454870-71454871
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 98 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10132789	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10132984	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10140225	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10140917	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10145824	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10147068	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10148324	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10150408	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs116016	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11623266	0.92[EUR][1000 genomes]
rs12893492	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12896829	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1468470	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1558097	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1978164	0.90[EUR][1000 genomes]
rs2010713	0.91[EUR][1000 genomes]
rs2097975	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs221904	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs221906	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs221908	0.84[AMR][1000 genomes]
rs221913	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs221914	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs221915	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs221916	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs221917	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs221918	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs221919	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs221924	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs221925	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs221926	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2240341	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2240531	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2251394	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2286311	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2332506	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2332507	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2526847	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2526848	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2526856	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2526859	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2526864	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2526871	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2526873	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2526875	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2526880	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2526883	0.90[EUR][1000 genomes]
rs2526884	0.89[EUR][1000 genomes]
rs2810072	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2810074	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2810077	0.83[EUR][1000 genomes]
rs2810078	0.89[EUR][1000 genomes]
rs2810079	0.84[EUR][1000 genomes]
rs2810101	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2810109	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2810111	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2810113	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2810118	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2877708	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2877714	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34542576	0.80[ASN][1000 genomes]
rs3784067	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4132848	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4366661	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4467005	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4531677	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58938327	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6573994	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs714421	0.84[EUR][1000 genomes]
rs7144986	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7145285	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7147862	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7150037	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7152845	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7154395	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7154437	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7156009	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7160958	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8004452	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8006046	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8007425	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8008111	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8020480	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8021824	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs917067	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9323556	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9323557	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9806042	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][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
rs4147077	PCNX	cis	Thyroid	GTEx
rs4147077	PCNX	cis	Artery Aorta	GTEx
rs4147077	PCNX	cis	Nerve Tibial	GTEx
rs4147077	PCNX	Cis_1M	lymphoblastoid	RTeQTL
rs4147077	PCNX	cis	Skin Sun Exposed Lower leg	GTEx
rs4147077	PCNX	cis	Artery Tibial	GTEx

Chromatin state (count:117 , 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	chr14:71433200-71455200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr14:71437200-71485600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr14:71438600-71502800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr14:71439200-71478000	Weak transcription	Colon Smooth Muscle	Colon
6	chr14:71439600-71502800	Weak transcription	Small Intestine	intestine
7	chr14:71445000-71461800	Weak transcription	A549	lung
8	chr14:71445200-71462400	Weak transcription	Esophagus	oesophagus
9	chr14:71445200-71462400	Weak transcription	Gastric	stomach
10	chr14:71445200-71462400	Weak transcription	Lung	lung
11	chr14:71445200-71470800	Weak transcription	GM12878-XiMat	blood
12	chr14:71445200-71471000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr14:71445200-71496200	Weak transcription	Fetal Brain Male	brain
14	chr14:71445200-71497800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr14:71445200-71502800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr14:71445200-71510800	Weak transcription	Colonic Mucosa	Colon
17	chr14:71445400-71455200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr14:71445400-71455200	Weak transcription	Aorta	Aorta
19	chr14:71445400-71455200	Weak transcription	Pancreas	Pancrea
20	chr14:71445400-71455200	Weak transcription	Right Ventricle	heart
21	chr14:71445400-71455200	Weak transcription	Spleen	Spleen
22	chr14:71445400-71456200	Weak transcription	Fetal Intestine Small	intestine
23	chr14:71445400-71462200	Weak transcription	Stomach Smooth Muscle	stomach
24	chr14:71445400-71462400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr14:71445400-71462400	Weak transcription	Ovary	ovary
26	chr14:71445400-71462400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr14:71445400-71465200	Weak transcription	Fetal Thymus	thymus
28	chr14:71445400-71468600	Weak transcription	Fetal Muscle Trunk	muscle
29	chr14:71445400-71470600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr14:71445400-71470600	Weak transcription	Fetal Stomach	stomach
31	chr14:71445400-71470800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr14:71445400-71471000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr14:71445400-71471000	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr14:71445400-71471000	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr14:71445400-71479600	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr14:71445400-71479800	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr14:71445400-71479800	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr14:71445400-71479800	Weak transcription	Thymus	Thymus
39	chr14:71445400-71479800	Weak transcription	HSMMtube	muscle
40	chr14:71445400-71480400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr14:71445400-71480400	Weak transcription	Left Ventricle	heart
42	chr14:71445400-71485600	Weak transcription	Brain Cingulate Gyrus	brain
43	chr14:71445400-71498000	Weak transcription	Brain Hippocampus Middle	brain
44	chr14:71445400-71502800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr14:71445600-71461800	Weak transcription	HepG2	liver
46	chr14:71445600-71462400	Weak transcription	Hela-S3	cervix
47	chr14:71445600-71464000	Weak transcription	Primary B cells from peripheral blood	blood
48	chr14:71445600-71464600	Weak transcription	Brain Substantia Nigra	brain
49	chr14:71445600-71468400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr14:71445600-71477400	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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