Variant report

Variant	rs3754878
Chromosome Location	chr2:99179384-99179385
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:99178906..99179443-chr2:99218109..99218671,2	MCF-7	breast:
2	chr2:99176672..99179836-chr2:99223007..99225878,3	K562	blood:
3	chr2:99177894..99180099-chr2:99183074..99185051,2	K562	blood:
4	chr2:99177928..99179821-chr2:99209901..99211618,2	K562	blood:

Variant related genes	Relation type
ENSG00000183513	Chromatin interaction
ENSG00000115446	Chromatin interaction

Extended variants
information (count: 167 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:164)

rs_ID	r²[population]
rs10199199	0.84[EUR][1000 genomes]
rs10496327	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10514774	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1139829	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11537554	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[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];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11884553	0.85[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11888595	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11892744	0.81[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11896729	0.95[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11901568	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11902825	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12052639	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12617721	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12618524	1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12619665	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12622341	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13402379	0.95[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1516085	0.95[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1587835	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17031139	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17031146	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17031905	0.90[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17032120	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17032866	0.90[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17032870	0.90[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17033136	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17033813	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17034171	0.95[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17034241	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17444095	0.90[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17446058	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17502889	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17504774	0.90[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.88[MKK][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17505088	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17505326	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17506535	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17513468	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1847550	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2230388	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2276603	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[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];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2278206	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2278207	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2278208	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2278211	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2278212	0.90[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2278213	0.81[ASW][hapmap];0.90[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.85[LWK][hapmap];0.84[MEX][hapmap];0.86[MKK][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2278214	0.90[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2309390	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3203856	0.89[ASW][hapmap];0.90[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34906456	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3729568	0.90[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3754871	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3754872	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3754875	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3754877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3754879	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3754880	0.90[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3754881	0.90[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3754883	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3754884	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3754885	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3754886	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3754888	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3754889	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3754890	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3754891	0.90[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3754892	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs3754893	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3769698	0.95[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3769701	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3769708	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3769709	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3769712	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3769713	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3769715	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3769716	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3769717	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3769719	0.90[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3769723	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3769724	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3769725	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3769726	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3769727	0.88[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3769728	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3769729	0.90[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3769730	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3769733	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3769734	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3769735	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3769736	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3769737	0.89[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.90[MKK][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3769738	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3769740	0.90[CEU][hapmap];0.88[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3769741	0.90[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3769743	0.90[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3820941	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3820943	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3820945	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4596026	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4599165	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4850874	0.90[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4850875	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4850876	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4850877	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4850878	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4850879	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4851131	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4851136	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4851138	0.90[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap]
rs4851140	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4851141	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4851142	0.90[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4851144	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4851145	0.95[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4851146	0.95[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55900716	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55934321	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56091613	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56118505	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56141907	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56197140	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56232707	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56240302	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56333112	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56357378	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58778964	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61180742	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6542754	0.82[EUR][1000 genomes]
rs6728891	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6736755	0.95[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6753380	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6753515	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72819965	0.84[EUR][1000 genomes]
rs72819970	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72819971	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72819972	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72819981	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72819996	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72820002	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72821904	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72821907	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72821908	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72821920	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72821924	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72821930	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72821939	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72821943	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72821946	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72821951	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72821955	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72821956	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72821965	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72823788	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72823792	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72823794	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72823796	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72823801	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7562232	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7585747	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7585939	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7588254	0.95[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7593615	0.84[EUR][1000 genomes]
rs7595120	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs961242	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006328	chr2:98977192-99210376	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1013941	chr2:99116255-99317933	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv535834	chr2:99116255-99317933	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3754878	MGAT4A	cis	cerebellum	SCAN
rs3754878	UNC50	cis	lymphoblastoid	seeQTL
rs3754878	ACTR1B	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99136400-99185400	Weak transcription	Hela-S3	cervix
2	chr2:99147200-99200200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:99148400-99211200	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr2:99149000-99209800	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr2:99149000-99210800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr2:99149200-99210800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr2:99156400-99197000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:99157200-99179600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr2:99158800-99190600	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr2:99159800-99201600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr2:99163000-99215000	Weak transcription	HMEC	breast
12	chr2:99163400-99180800	Weak transcription	Fetal Brain Male	brain
13	chr2:99163800-99194000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr2:99164400-99210800	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr2:99167600-99193400	Weak transcription	Fetal Heart	heart
16	chr2:99168000-99205200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr2:99168400-99210400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr2:99168600-99197600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr2:99169000-99181600	Weak transcription	A549	lung
20	chr2:99169400-99185200	Weak transcription	Fetal Kidney	kidney
21	chr2:99169400-99222600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr2:99169600-99184400	Weak transcription	NHEK	skin
23	chr2:99170800-99181200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:99171200-99182200	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr2:99171600-99179800	Weak transcription	Colonic Mucosa	Colon
26	chr2:99172000-99183600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr2:99172400-99180000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr2:99172800-99181000	Weak transcription	Small Intestine	intestine
29	chr2:99173000-99179400	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr2:99173000-99179800	Weak transcription	Gastric	stomach
31	chr2:99173000-99180600	Weak transcription	Pancreas	Pancrea
32	chr2:99173000-99181200	Weak transcription	Brain Substantia Nigra	brain
33	chr2:99173000-99186000	Weak transcription	Stomach Mucosa	stomach
34	chr2:99173200-99179600	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr2:99173200-99205000	Strong transcription	Primary T cells from cord blood	blood
36	chr2:99173400-99179800	Weak transcription	Fetal Lung	lung
37	chr2:99173400-99181200	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr2:99173400-99204800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr2:99174000-99180400	Weak transcription	Brain Hippocampus Middle	brain
40	chr2:99174000-99204000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
41	chr2:99174600-99180800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr2:99174600-99207800	Weak transcription	HUVEC	blood vessel
43	chr2:99174800-99179600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr2:99175400-99179600	Enhancers	Colon Smooth Muscle	Colon
45	chr2:99175600-99179600	Enhancers	NHLF	lung
46	chr2:99175800-99181000	Strong transcription	Fetal Brain Female	brain
47	chr2:99176000-99179400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr2:99176000-99179800	Weak transcription	Duodenum Mucosa	Duodenum
49	chr2:99176000-99180000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:99176000-99180600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links