Variant report

Variant	rs2117938
Chromosome Location	chr3:49263850-49263851
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 42 )

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

rs_ID	r²[population]
rs10049462	1.00[JPT][hapmap]
rs10865954	0.89[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11130182	0.82[EUR][1000 genomes]
rs11130184	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11130185	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11552724	1.00[JPT][hapmap]
rs11706052	1.00[JPT][hapmap]
rs11706189	1.00[JPT][hapmap]
rs11710247	0.92[ASN][1000 genomes]
rs11713297	1.00[JPT][hapmap]
rs11715581	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11716334	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11717524	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719220	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11720460	0.92[ASN][1000 genomes]
rs11920267	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12490393	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12493001	0.89[CEU][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap]
rs12629637	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12629759	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12631989	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12637576	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13064780	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13068038	1.00[JPT][hapmap]
rs13077498	1.00[JPT][hapmap]
rs2304442	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2334958	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3212	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]
rs34566463	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs34580506	1.00[JPT][hapmap]
rs34784192	0.92[ASN][1000 genomes]
rs35060561	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs35174559	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35185152	0.86[ASN][1000 genomes]
rs35218722	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35283189	1.00[JPT][hapmap]
rs35673421	1.00[JPT][hapmap]
rs3774800	0.96[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs4279134	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]
rs4308307	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4367098	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4499638	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4513485	0.84[ASW][hapmap];0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap]
rs4521268	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs4536858	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4955410	0.84[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap]
rs4955418	0.92[CEU][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4955419	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4955420	0.89[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs4955432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5030795	1.00[JPT][hapmap]
rs55713230	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61583136	0.81[EUR][1000 genomes]
rs67286839	0.92[ASN][1000 genomes]
rs6779394	0.89[CEU][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]
rs6784111	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs6790914	0.81[EUR][1000 genomes]
rs6794924	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6795756	0.93[EUR][1000 genomes]
rs6795772	0.91[LWK][hapmap];0.98[MKK][hapmap]
rs71324939	0.95[ASN][1000 genomes]
rs7432989	0.85[CEU][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs7626445	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs7638154	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7652746	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9311439	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9814987	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9826525	0.92[ASN][1000 genomes]
rs9837237	1.00[JPT][hapmap]
rs9837625	1.00[JPT][hapmap]
rs9840050	0.85[CEU][hapmap];0.82[CHB][hapmap];0.83[TSI][hapmap]
rs9846123	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs9847839	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9850917	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9880088	1.00[JPT][hapmap]
rs9880309	1.00[JPT][hapmap]
rs9990153	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834686	chr3:49106047-49270556	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1008750	chr3:49208815-49362401	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:42)

SNP	Gene	Cis/trans	Tissue	Source
rs2117938	WDR6	cis	Adipose Subcutaneous	GTEx
rs2117938	C3orf62	cis	cerebellum	SCAN
rs2117938	NCKIPSD	cis	cerebellum	SCAN
rs2117938	NCKIPSD	cis	Muscle Skeletal	GTEx
rs2117938	WDR6	cis	multi-tissue	Pritchard
rs2117938	DALRD3	cis	cerebellum	SCAN
rs2117938	WDR6	cis	Heart Left Ventricle	GTEx
rs2117938	CCDC71	cis	cerebellum	SCAN
rs2117938	AMT	cis	parietal	SCAN
rs2117938	AMT	cis	Muscle Skeletal	GTEx
rs2117938	CXorf38	trans	parietal	SCAN
rs2117938	AMT	cis	Thyroid	GTEx
rs2117938	AMT	cis	Whole Blood	GTEx
rs2117938	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs2117938	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs2117938	ARIH2	cis	Thyroid	GTEx
rs2117938	WDR6	cis	Whole Blood	GTEx
rs2117938	NCKIPSD	cis	multi-tissue	Pritchard
rs2117938	WDR6	cis	cerebellum	SCAN
rs2117938	SEMA3G	cis	cerebellum	SCAN
rs2117938	AMT	cis	cerebellum	SCAN
rs2117938	WDR6	cis	Esophagus Muscularis	GTEx
rs2117938	NCKIPSD	cis	parietal	SCAN
rs2117938	WDR6	cis	Muscle Skeletal	GTEx
rs2117938	P4HTM	cis	parietal	SCAN
rs2117938	WDR6	cis	lymphoblastoid	seeQTL
rs2117938	AMT	cis	Artery Aorta	GTEx
rs2117938	WDR6	cis	parietal	SCAN
rs2117938	AMT	cis	multi-tissue	Pritchard
rs2117938	NICN1-AS1	cis	Thyroid	GTEx
rs2117938	WDR6	cis	Artery Tibial	GTEx
rs2117938	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs2117938	WDR6	cis	Esophagus Mucosa	GTEx
rs2117938	P4HTM	cis	cerebellum	SCAN
rs2117938	WDR6	cis	lung	GTEx
rs2117938	NICN1	cis	Thyroid	GTEx
rs2117938	TLR9	cis	parietal	SCAN
rs2117938	WDR6	cis	Nerve Tibial	GTEx
rs2117938	NICN1	cis	multi-tissue	Pritchard
rs2117938	CCDC36	cis	Artery Tibial	GTEx
rs2117938	ZNF589	cis	parietal	SCAN
rs2117938	CCDC36	cis	Esophagus Muscularis	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49250200-49274000	Weak transcription	Osteobl	bone
2	chr3:49251600-49265400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:49252000-49265600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr3:49255800-49264800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr3:49255800-49265600	Weak transcription	Aorta	Aorta
6	chr3:49256600-49265400	Weak transcription	Fetal Heart	heart
7	chr3:49256600-49275800	Weak transcription	NHLF	lung
8	chr3:49256800-49264000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:49256800-49264600	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr3:49256800-49265200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:49256800-49265200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr3:49256800-49266000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr3:49258000-49264200	Weak transcription	Adipose Nuclei	Adipose
14	chr3:49263200-49264600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr3:49263400-49269400	Weak transcription	Ovary	ovary

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