Variant report

Variant	rs1663556
Chromosome Location	chr3:138396850-138396851
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 150 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:141)

rs_ID	r²[population]
rs1066197	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1068104	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1068685	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11705762	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709768	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713049	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11717457	0.86[EUR][1000 genomes]
rs11720178	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11924814	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13069296	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13082808	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13433948	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1400266	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1663554	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1673597	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs168633	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs181729	0.91[EUR][1000 genomes]
rs187245	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs191713	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs191714	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs191775	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2197387	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2348147	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs244380	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs244381	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2595928	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2595930	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2595932	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2607108	0.89[ASN][1000 genomes]
rs2607109	0.89[ASN][1000 genomes]
rs2607796	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28376988	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28408150	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34900559	0.89[ASN][1000 genomes]
rs35214574	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361054	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361055	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361056	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361057	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs361059	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361060	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361061	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs361062	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361063	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361064	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361065	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361066	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361067	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361068	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361069	0.84[EUR][1000 genomes]
rs361071	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361072	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361079	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361080	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361081	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361082	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361083	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361084	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361085	0.89[ASN][1000 genomes]
rs361086	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs361087	0.85[EUR][1000 genomes]
rs361088	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs361089	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs361092	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs361094	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361096	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361097	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs371762	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs385254	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs398065	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs404110	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs409507	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs413147	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs425901	0.88[EUR][1000 genomes]
rs4305444	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs439720	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs448808	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs470359	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs473388	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs475254	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs476800	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs482334	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894350	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894351	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894352	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894353	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894354	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs491371	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs493152	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs497900	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs500687	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs511207	0.92[EUR][1000 genomes]
rs524164	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs531577	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs537894	0.81[AMR][1000 genomes]
rs539156	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs539619	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs540198	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs540907	0.88[EUR][1000 genomes]
rs550768	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs558905	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs559160	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs559451	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs564455	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs574942	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs589986	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs600590	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs603723	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs607044	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs618457	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs621204	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62282169	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs624099	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs625468	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs635592	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6439817	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439819	0.89[EUR][1000 genomes]
rs647972	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs654459	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6776585	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6781914	0.83[EUR][1000 genomes]
rs6794270	0.81[EUR][1000 genomes]
rs6795203	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6801207	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6810351	0.91[EUR][1000 genomes]
rs7612106	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615854	0.81[EUR][1000 genomes]
rs7643722	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs772612	0.91[EUR][1000 genomes]
rs773045	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs773184	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9821694	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9822714	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9823213	0.89[EUR][1000 genomes]
rs9832012	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9834963	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9853819	0.88[EUR][1000 genomes]
rs9863481	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9864176	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9874723	1.00[ASN][1000 genomes]
rs9879784	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1663556	PIK3CB	Cis_1M	lymphoblastoid	RTeQTL
rs1663556	FAIM	cis	Muscle Skeletal	GTEx
rs1663556	CEP70	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138360800-138407600	Weak transcription	HUVEC	blood vessel
2	chr3:138364400-138459200	Weak transcription	Psoas Muscle	Psoas
3	chr3:138368800-138400200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr3:138368800-138422600	Weak transcription	Right Atrium	heart
5	chr3:138369000-138493000	Weak transcription	Fetal Lung	lung
6	chr3:138369200-138401600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:138369200-138412800	Weak transcription	Hela-S3	cervix
8	chr3:138369200-138428800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:138369200-138435600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:138374800-138397000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr3:138375200-138429000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:138383000-138404800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:138383200-138412800	Weak transcription	Ovary	ovary
14	chr3:138383200-138448200	Weak transcription	Gastric	stomach
15	chr3:138383400-138426400	Weak transcription	Spleen	Spleen
16	chr3:138383400-138443000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr3:138383800-138400200	Weak transcription	Fetal Kidney	kidney
18	chr3:138383800-138405400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr3:138385000-138418400	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr3:138388400-138399600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:138389200-138401200	Weak transcription	Brain Substantia Nigra	brain
22	chr3:138389200-138405000	Weak transcription	Small Intestine	intestine
23	chr3:138390800-138459600	Weak transcription	Right Ventricle	heart
24	chr3:138391200-138422000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr3:138392200-138405600	Weak transcription	Stomach Mucosa	stomach
26	chr3:138392600-138397400	Strong transcription	Fetal Thymus	thymus
27	chr3:138393200-138397200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:138393200-138399600	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr3:138393200-138401000	Weak transcription	Brain Angular Gyrus	brain
30	chr3:138393200-138405600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr3:138393200-138407800	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr3:138393400-138399800	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr3:138393600-138400200	Weak transcription	HepG2	liver
34	chr3:138393600-138405600	Weak transcription	HSMM	muscle
35	chr3:138393800-138515000	Weak transcription	Aorta	Aorta
36	chr3:138394000-138401000	Weak transcription	Left Ventricle	heart
37	chr3:138394000-138404800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr3:138394000-138418600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:138394200-138397200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
40	chr3:138394400-138397400	ZNF genes & repeats	K562	blood
41	chr3:138394400-138413000	Weak transcription	Colon Smooth Muscle	Colon
42	chr3:138394600-138397200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr3:138394800-138397200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr3:138395000-138397200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
45	chr3:138395000-138397200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr3:138395200-138397200	Strong transcription	Adipose Nuclei	Adipose
47	chr3:138395200-138398000	Strong transcription	Placenta	Placenta
48	chr3:138395200-138436800	Weak transcription	Brain Germinal Matrix	brain
49	chr3:138395400-138400200	Weak transcription	Fetal Heart	heart
50	chr3:138395400-138402200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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