Variant report

Variant	rs4894353
Chromosome Location	chr3:138515083-138515084
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 154 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:143)

rs_ID	r²[population]
rs1066197	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1068104	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1068685	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11705762	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709768	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713049	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11717457	0.86[EUR][1000 genomes]
rs11720178	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11924814	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13069296	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13082808	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13433948	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1400266	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1663554	0.90[ASN][1000 genomes]
rs1663556	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1673597	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs168633	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs181729	0.88[EUR][1000 genomes]
rs187245	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs191713	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs191714	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs191775	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2197387	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2348147	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs244380	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs244381	0.90[EUR][1000 genomes]
rs2595928	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2595930	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2595932	1.00[ASN][1000 genomes]
rs2607108	0.89[ASN][1000 genomes]
rs2607109	0.89[ASN][1000 genomes]
rs2607796	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28376988	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28408150	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2881900	0.81[EUR][1000 genomes]
rs34900559	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35214574	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361054	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361055	1.00[ASN][1000 genomes]
rs361056	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs361057	0.87[EUR][1000 genomes]
rs361059	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361060	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361061	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs361062	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361063	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361064	1.00[ASN][1000 genomes]
rs361065	1.00[ASN][1000 genomes]
rs361066	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361067	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361068	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361069	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs361071	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361072	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361079	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs361080	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361081	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361082	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361083	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361084	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361085	0.89[ASN][1000 genomes]
rs361088	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs361089	0.88[EUR][1000 genomes]
rs361092	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs361094	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361096	1.00[ASN][1000 genomes]
rs361097	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs371762	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs385254	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs398065	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs404110	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs409507	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs413147	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs425901	0.92[EUR][1000 genomes]
rs4305444	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs439720	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs448808	0.90[EUR][1000 genomes]
rs470359	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs473388	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs475254	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs476800	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs482334	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894350	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894351	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894352	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894354	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs491371	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs493152	1.00[ASN][1000 genomes]
rs497900	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs500687	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs511207	0.95[EUR][1000 genomes]
rs524164	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs531577	1.00[ASN][1000 genomes]
rs539156	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs539619	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs540198	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs540907	0.92[EUR][1000 genomes]
rs550768	0.87[EUR][1000 genomes]
rs558905	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs559160	0.89[EUR][1000 genomes]
rs559451	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs564455	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs574942	1.00[ASN][1000 genomes]
rs589986	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs603723	0.89[EUR][1000 genomes]
rs607044	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs618457	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs621204	0.87[EUR][1000 genomes]
rs62282169	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs624099	0.88[EUR][1000 genomes]
rs625468	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs635592	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6439817	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439819	0.93[EUR][1000 genomes]
rs647972	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs654459	0.81[EUR][1000 genomes]
rs6776585	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6780989	0.81[AMR][1000 genomes]
rs6781914	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6784610	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6794270	0.85[EUR][1000 genomes]
rs6795203	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6801207	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6810351	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7612106	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643722	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs772612	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs773045	0.89[EUR][1000 genomes]
rs773184	0.87[EUR][1000 genomes]
rs9647336	0.82[AFR][1000 genomes]
rs9647337	0.82[AFR][1000 genomes]
rs9818354	0.81[EUR][1000 genomes]
rs9821694	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9822714	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9823213	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9832012	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9834963	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9853819	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9863481	0.81[EUR][1000 genomes]
rs9864176	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9874723	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9877108	0.84[EUR][1000 genomes]
rs9879784	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[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	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1013074	chr3:138213166-138737688	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1002612	chr3:138213274-138831792	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv536726	chr3:138213274-138831792	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1009726	chr3:138219923-138737688	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv869205	chr3:138248190-138775288	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv868955	chr3:138248190-138848947	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv591854	chr3:138348081-138764229	Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv1010514	chr3:138365640-138737688	Flanking Bivalent TSS/Enh Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv1000927	chr3:138423543-138632596	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking 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	16 gene(s)	inside rSNPs	diseases
11	nsv917964	chr3:138440701-138699084	Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4894353	PIK3CB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138488000-138519200	Weak transcription	Spleen	Spleen
2	chr3:138489200-138519200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr3:138492400-138515800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr3:138494600-138515800	Weak transcription	Ovary	ovary
5	chr3:138494600-138518600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:138494600-138521200	Weak transcription	Right Ventricle	heart
7	chr3:138494800-138537000	Weak transcription	HUVEC	blood vessel
8	chr3:138495600-138517600	Weak transcription	HSMMtube	muscle
9	chr3:138496200-138516200	Weak transcription	Fetal Muscle Trunk	muscle
10	chr3:138496200-138521400	Weak transcription	Brain Anterior Caudate	brain
11	chr3:138496200-138522400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr3:138496400-138515600	Weak transcription	Psoas Muscle	Psoas
13	chr3:138497400-138515800	Weak transcription	Gastric	stomach
14	chr3:138497800-138516600	Weak transcription	Right Atrium	heart
15	chr3:138501200-138534200	Weak transcription	Dnd41	blood
16	chr3:138501600-138515800	Weak transcription	Fetal Heart	heart
17	chr3:138501600-138532800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr3:138502000-138522400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr3:138504000-138552000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr3:138505000-138522200	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr3:138505400-138516800	Strong transcription	Fetal Intestine Small	intestine
22	chr3:138505600-138526400	Weak transcription	Brain Germinal Matrix	brain
23	chr3:138505800-138522200	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr3:138506000-138521600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr3:138506000-138525600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr3:138506000-138542200	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr3:138506000-138551800	Weak transcription	Primary B cells from cord blood	blood
28	chr3:138506200-138516600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr3:138506200-138518600	Weak transcription	Brain Hippocampus Middle	brain
30	chr3:138506200-138520400	Weak transcription	Osteobl	bone
31	chr3:138506400-138521800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:138506400-138536800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:138506600-138537000	Weak transcription	Primary hematopoietic stem cells	blood
34	chr3:138506800-138527200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr3:138507200-138517400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr3:138509600-138516800	Weak transcription	Colon Smooth Muscle	Colon
37	chr3:138509800-138522400	Weak transcription	Small Intestine	intestine
38	chr3:138510000-138515400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:138510600-138526400	Weak transcription	Pancreas	Pancrea
40	chr3:138510600-138530600	Weak transcription	Fetal Stomach	stomach
41	chr3:138510800-138516200	Weak transcription	GM12878-XiMat	blood
42	chr3:138510800-138522200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr3:138511000-138534400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr3:138511800-138516200	Weak transcription	Stomach Mucosa	stomach
45	chr3:138512000-138542800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr3:138512400-138536800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr3:138512600-138521800	Weak transcription	HMEC	breast
48	chr3:138512600-138534000	Weak transcription	Primary B cells from peripheral blood	blood
49	chr3:138512800-138515800	Weak transcription	Left Ventricle	heart
50	chr3:138512800-138516600	Weak transcription	Primary T helper cells PMA-I stimulated	--

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