Variant report

Variant	rs12493001
Chromosome Location	chr3:49181885-49181886
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 102 )
Associated
traits (count: 36 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10049462	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10154895	1.00[ASN][1000 genomes]
rs10865954	0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.89[ASN][1000 genomes]
rs11130182	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11130184	0.89[CEU][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11552724	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11706052	1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11706189	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11712006	0.89[ASN][1000 genomes]
rs11713297	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11715581	0.96[CEU][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11716334	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11719220	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11920267	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs12487580	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12490393	0.94[ASW][hapmap];0.96[CEU][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.89[MEX][hapmap];0.85[MKK][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12629759	0.89[CEU][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12631989	0.92[CEU][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap]
rs12636030	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12637576	0.89[CEU][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.83[YRI][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13064784	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13068038	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs13072554	0.81[ASN][1000 genomes]
rs13077498	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs13080725	0.81[ASN][1000 genomes]
rs13086240	1.00[JPT][hapmap]
rs13096406	0.92[ASN][1000 genomes]
rs13315711	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs13316620	0.92[CEU][hapmap]
rs2117938	0.89[CEU][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap]
rs2304442	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs3212	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34326553	0.89[ASN][1000 genomes]
rs34566463	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs34580506	0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs34889065	0.89[ASN][1000 genomes]
rs35060561	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs35108630	0.81[ASN][1000 genomes]
rs35174559	0.92[CEU][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap]
rs35283189	1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs35673421	1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs36133651	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3774800	0.92[CEU][hapmap]
rs3923475	0.81[ASN][1000 genomes]
rs4279134	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4308307	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4364202	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4499638	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4513485	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4521268	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4536858	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4955410	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4955418	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.89[MEX][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4955419	0.96[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4955420	0.87[CHD][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.86[YRI][hapmap];0.92[ASN][1000 genomes]
rs4955432	0.89[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs4974078	0.87[CHD][hapmap]
rs4974080	0.96[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap]
rs4974082	0.96[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs5030795	1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs55713230	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61583136	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62262517	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6414613	0.96[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap]
rs6446196	0.88[ASW][hapmap];0.96[CEU][hapmap];0.81[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap]
rs6446205	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap]
rs66991555	0.89[ASN][1000 genomes]
rs6768433	0.95[CEU][hapmap]
rs6770112	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6779394	0.88[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6781790	0.96[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap]
rs6784111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs6790914	0.97[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6794924	0.87[ASN][1000 genomes]
rs6795025	0.81[ASN][1000 genomes]
rs7430198	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap]
rs7432989	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes]
rs7615235	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7621015	0.96[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap]
rs7626445	0.96[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7628719	0.96[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs7632267	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7643368	0.96[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap]
rs7645551	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7652746	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs9311439	1.00[JPT][hapmap]
rs9683094	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9814987	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9835439	0.94[ASN][1000 genomes]
rs9837237	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9837625	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9840050	0.96[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9846123	0.96[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap]
rs9847839	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9850917	1.00[JPT][hapmap]
rs9855123	0.94[ASN][1000 genomes]
rs9862483	1.00[ASN][1000 genomes]
rs9880088	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9880309	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9990153	1.00[CHB][hapmap];1.00[CHD][hapmap];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	nsv876764	chr3:49040462-49245645	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	279 gene(s)	inside rSNPs	diseases
2	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

mRNA abundance (count:36)

SNP	Gene	Cis/trans	Tissue	Source
rs12493001	NICN1-AS1	cis	Thyroid	GTEx
rs12493001	AMT	cis	Whole Blood	GTEx
rs12493001	P4HTM	cis	parietal	SCAN
rs12493001	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs12493001	WDR6	cis	lung	GTEx
rs12493001	WDR6	cis	Whole Blood	GTEx
rs12493001	AMT	cis	cerebellum	SCAN
rs12493001	WDR6	cis	Muscle Skeletal	GTEx
rs12493001	WDR6	cis	cerebellum	SCAN
rs12493001	TLR9	cis	parietal	SCAN
rs12493001	DALRD3	cis	cerebellum	SCAN
rs12493001	WDR6	cis	parietal	SCAN
rs12493001	NCKIPSD	cis	cerebellum	SCAN
rs12493001	WDR6	cis	Esophagus Muscularis	GTEx
rs12493001	P4HTM	cis	cerebellum	SCAN
rs12493001	NCKIPSD	cis	Whole Blood	GTEx
rs12493001	NCKIPSD	cis	Muscle Skeletal	GTEx
rs12493001	ARIH2	Cis_1M	lymphoblastoid	RTeQTL
rs12493001	WDR6	cis	Stomach	GTEx
rs12493001	WDR6	cis	lymphoblastoid	seeQTL
rs12493001	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs12493001	AMT	cis	Thyroid	GTEx
rs12493001	NCKIPSD	cis	parietal	SCAN
rs12493001	WDR6	cis	Adipose Subcutaneous	GTEx
rs12493001	CCDC36	cis	Artery Tibial	GTEx
rs12493001	AMT	cis	Muscle Skeletal	GTEx
rs12493001	WDR6	cis	Nerve Tibial	GTEx
rs12493001	NCKIPSD	cis	Nerve Tibial	GTEx
rs12493001	PHF7	cis	parietal	SCAN
rs12493001	CCDC71	cis	cerebellum	SCAN
rs12493001	WDR6	cis	Heart Left Ventricle	GTEx
rs12493001	CCDC36	cis	Esophagus Muscularis	GTEx
rs12493001	NICN1	cis	Thyroid	GTEx
rs12493001	WDR6	cis	Artery Tibial	GTEx
rs12493001	WDR6	cis	Esophagus Mucosa	GTEx
rs12493001	AMT	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49172200-49200400	Weak transcription	Colon Smooth Muscle	Colon
2	chr3:49179400-49182600	Weak transcription	Thymus	Thymus
3	chr3:49179800-49182000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:49179800-49187400	Weak transcription	Esophagus	oesophagus
5	chr3:49181200-49185800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:49181600-49182200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin

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