Variant report

Variant	rs550768
Chromosome Location	chr3:138361025-138361026
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 143 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:134)

rs_ID	r²[population]
rs1066197	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1068104	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1068685	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11705762	0.89[EUR][1000 genomes]
rs11709768	0.90[EUR][1000 genomes]
rs11713049	0.89[EUR][1000 genomes]
rs11717457	0.84[EUR][1000 genomes]
rs11720178	0.84[EUR][1000 genomes]
rs11924814	0.89[EUR][1000 genomes]
rs13069296	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13082808	0.88[EUR][1000 genomes]
rs13433948	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1400266	0.89[EUR][1000 genomes]
rs1663554	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1663556	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1673597	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs168633	0.87[EUR][1000 genomes]
rs181729	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs187245	0.82[EUR][1000 genomes]
rs191713	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs191714	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs191775	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2197387	0.91[EUR][1000 genomes]
rs2348147	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs244380	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs244381	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2595928	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2595930	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2595932	0.86[EUR][1000 genomes]
rs2607796	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28376988	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28408150	0.89[EUR][1000 genomes]
rs35214574	0.86[EUR][1000 genomes]
rs361054	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs361055	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs361056	0.85[EUR][1000 genomes]
rs361057	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361059	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs361060	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs361061	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs361062	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs361063	0.98[EUR][1000 genomes]
rs361064	0.85[EUR][1000 genomes]
rs361065	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs361066	0.91[EUR][1000 genomes]
rs361067	0.91[EUR][1000 genomes]
rs361068	0.91[EUR][1000 genomes]
rs361069	0.83[EUR][1000 genomes]
rs361071	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs361072	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs361080	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs361081	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs361082	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs361083	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs361084	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs361086	0.83[EUR][1000 genomes]
rs361087	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361088	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs361089	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361092	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361094	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs361096	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs361097	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs371762	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs385254	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs398065	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs404110	0.91[EUR][1000 genomes]
rs409507	0.89[EUR][1000 genomes]
rs413147	0.89[EUR][1000 genomes]
rs425901	0.86[EUR][1000 genomes]
rs4305444	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs439720	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs448808	0.85[EUR][1000 genomes]
rs470359	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs473388	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs475254	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs476800	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs482334	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4894350	0.91[EUR][1000 genomes]
rs4894351	0.90[EUR][1000 genomes]
rs4894352	0.91[EUR][1000 genomes]
rs4894353	0.87[EUR][1000 genomes]
rs4894354	0.86[EUR][1000 genomes]
rs491371	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs493152	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs497900	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs500687	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs511207	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs524164	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs531577	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs539156	0.84[EUR][1000 genomes]
rs539619	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs540198	0.90[EUR][1000 genomes]
rs540907	0.87[EUR][1000 genomes]
rs558905	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs559160	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs559451	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs564455	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs574942	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs589986	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs600590	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs601032	1.00[ASN][1000 genomes]
rs603723	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs607044	0.91[EUR][1000 genomes]
rs618457	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs621204	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282169	0.83[EUR][1000 genomes]
rs624099	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs625468	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs635592	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439817	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6439819	0.88[EUR][1000 genomes]
rs647972	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs654459	0.89[EUR][1000 genomes]
rs6776585	0.89[EUR][1000 genomes]
rs6781914	0.81[EUR][1000 genomes]
rs6795203	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6801207	0.89[EUR][1000 genomes]
rs6810351	0.89[EUR][1000 genomes]
rs7612106	0.89[EUR][1000 genomes]
rs7641106	0.89[ASN][1000 genomes]
rs7643722	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs772612	0.90[EUR][1000 genomes]
rs773045	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773184	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9821694	0.91[EUR][1000 genomes]
rs9822714	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9823213	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9832012	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9834963	0.89[EUR][1000 genomes]
rs9853819	0.87[EUR][1000 genomes]
rs9863481	0.81[EUR][1000 genomes]
rs9864176	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9879784	0.85[EUR][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	nsv967070	chr3:138355155-138372373	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs550768	CEP70	Cis_1M	lymphoblastoid	RTeQTL
rs550768	PIK3CB	Cis_1M	lymphoblastoid	RTeQTL
rs550768	FAIM	cis	Muscle Skeletal	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138335400-138368000	Weak transcription	Right Ventricle	heart
2	chr3:138340400-138393800	Weak transcription	Fetal Brain Male	brain
3	chr3:138342400-138362200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:138345000-138367800	Weak transcription	HSMM	muscle
5	chr3:138345400-138361600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:138345400-138368000	Weak transcription	NHLF	lung
7	chr3:138345600-138367400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr3:138345800-138368000	Weak transcription	HMEC	breast
9	chr3:138348800-138368000	Weak transcription	Hela-S3	cervix
10	chr3:138349000-138367400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr3:138349000-138368000	Weak transcription	Pancreas	Pancrea
12	chr3:138350800-138362800	Weak transcription	Thymus	Thymus
13	chr3:138350800-138367800	Weak transcription	Osteobl	bone
14	chr3:138351400-138367800	Weak transcription	Ovary	ovary
15	chr3:138353000-138361600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:138353000-138367800	Weak transcription	Fetal Kidney	kidney
17	chr3:138353000-138368200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:138358000-138368000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:138358000-138368000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:138360600-138372000	Weak transcription	NH-A	brain
21	chr3:138360800-138407600	Weak transcription	HUVEC	blood vessel
22	chr3:138361000-138361800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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