Variant report

Variant	rs17039940
Chromosome Location	chr2:50359270-50359271
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 142 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:133)

rs_ID	r²[population]
rs1037428	0.98[ASN][1000 genomes]
rs10490240	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10490243	1.00[CHB][hapmap]
rs10865243	0.93[ASN][1000 genomes]
rs11125288	0.99[ASN][1000 genomes]
rs11125289	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11125290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11125291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11125292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11125294	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11125295	0.87[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.87[TSI][hapmap]
rs11125296	0.92[CEU][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11883844	0.99[ASN][1000 genomes]
rs11887484	0.93[ASN][1000 genomes]
rs11888330	1.00[CEU][hapmap]
rs11896556	1.00[CEU][hapmap]
rs11898302	0.93[ASN][1000 genomes]
rs11900502	0.83[AMR][1000 genomes]
rs11901625	0.91[ASN][1000 genomes]
rs12151722	0.99[ASN][1000 genomes]
rs12151727	0.99[ASN][1000 genomes]
rs12465888	0.98[ASN][1000 genomes]
rs12466807	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs12468151	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12468252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12468282	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs12468342	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12468396	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12468477	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap]
rs12469244	0.90[ASN][1000 genomes]
rs12470002	1.00[CHB][hapmap]
rs12472712	1.00[CHB][hapmap]
rs12472743	1.00[CHB][hapmap];0.95[CHD][hapmap]
rs12473119	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs12474335	0.84[ASN][1000 genomes]
rs12475100	0.87[CEU][hapmap];1.00[YRI][hapmap]
rs12476530	0.81[CHB][hapmap]
rs12477934	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs12478732	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.81[MKK][hapmap];0.98[ASN][1000 genomes]
rs12479057	0.98[ASN][1000 genomes]
rs12613266	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12620250	0.86[ASN][1000 genomes]
rs12622844	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12622858	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.82[MEX][hapmap];0.99[ASN][1000 genomes]
rs12986904	1.00[CHB][hapmap]
rs1377233	0.84[CHB][hapmap]
rs1377238	1.00[CEU][hapmap];0.89[GIH][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap]
rs1421573	0.93[CEU][hapmap];0.91[YRI][hapmap]
rs1452769	1.00[CEU][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes]
rs1452770	0.86[AMR][1000 genomes]
rs1452771	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1452778	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs1452779	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs1452780	0.85[ASN][1000 genomes]
rs1452781	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs1452783	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs1517827	0.87[ASW][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.82[TSI][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1563019	1.00[CEU][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap]
rs1563020	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs1563024	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[ASN][1000 genomes]
rs1563026	1.00[CHB][hapmap];0.87[CHD][hapmap];0.86[ASN][1000 genomes]
rs1563027	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs1563028	1.00[CEU][hapmap]
rs1584763	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17039801	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[ASN][1000 genomes]
rs17039807	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs17039848	0.91[ASN][1000 genomes]
rs17039863	0.86[ASN][1000 genomes]
rs17039900	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17039905	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17039932	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][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]
rs17039935	1.00[ASN][1000 genomes]
rs17039947	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17039976	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs17039979	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs17039985	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17040013	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs17040034	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs17040064	0.87[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17040090	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17040117	1.00[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs17040123	1.00[CEU][hapmap]
rs17040138	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs17040141	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs17040147	1.00[CEU][hapmap];0.83[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes]
rs17040160	1.00[CEU][hapmap];0.83[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.80[AMR][1000 genomes]
rs17040169	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs1840074	0.92[ASN][1000 genomes]
rs1880075	0.93[ASN][1000 genomes]
rs1961358	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs2011317	0.86[ASN][1000 genomes]
rs2045003	0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[ASN][1000 genomes]
rs2123388	1.00[CHB][hapmap]
rs2176872	0.82[AMR][1000 genomes]
rs4641977	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs4971554	0.86[ASN][1000 genomes]
rs4971556	0.93[ASN][1000 genomes]
rs4971648	1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[ASN][1000 genomes]
rs4971649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4971650	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4971652	0.87[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.87[TSI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4971653	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4971654	0.80[AMR][1000 genomes]
rs4971655	1.00[CEU][hapmap]
rs4971656	1.00[CEU][hapmap];0.82[TSI][hapmap]
rs4971658	1.00[CEU][hapmap];0.80[AMR][1000 genomes]
rs4971659	1.00[CEU][hapmap];0.80[AMR][1000 genomes]
rs4971661	0.81[AMR][1000 genomes]
rs57366806	0.88[ASN][1000 genomes]
rs60500567	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61035060	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6712102	1.00[CEU][hapmap]
rs6712119	0.93[CEU][hapmap];0.82[GIH][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap]
rs6712423	1.00[CEU][hapmap]
rs6716404	1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[ASN][1000 genomes]
rs6731360	0.93[ASN][1000 genomes]
rs6731397	0.87[CEU][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs72874683	0.86[ASN][1000 genomes]
rs72874698	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs72878113	0.82[EUR][1000 genomes]
rs72878157	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72878159	0.99[ASN][1000 genomes]
rs72881242	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7590544	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs7599349	1.00[CEU][hapmap]
rs7607863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs896683	1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[LWK][hapmap];0.81[MKK][hapmap];0.91[ASN][1000 genomes]
rs896684	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs896685	0.93[ASN][1000 genomes]
rs921572	0.84[CHB][hapmap]
rs921573	0.84[CHB][hapmap]
rs930752	0.84[CHB][hapmap]
rs9917277	0.93[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	esv3388948	chr2:50092667-50602681	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
2	esv3399511	chr2:50092687-50602651	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv934303	chr2:50145598-50412189	Bivalent Enhancer Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv932915	chr2:50306630-50628415	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	esv2756107	chr2:50307245-50440043	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv948833	chr2:50307245-50459077	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv2756536	chr2:50313811-50375695	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1002344	chr2:50326207-50518933	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv535692	chr2:50326207-50518933	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17039940	ATP6V1E2	cis	parietal	SCAN
rs17039940	PRKCE	cis	cerebellum	SCAN
rs17039940	CRIPT	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:50353400-50360600	Weak transcription	Fetal Brain Male	brain
2	chr2:50358800-50359400	Enhancers	Pancreatic Islets	Pancreatic Islet

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