Variant report

Variant	rs3888
Chromosome Location	chr3:47857575-47857576
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47850679..47853675-chr3:47855656..47858435,3	K562	blood:
2	chr3:47857235..47858772-chr3:47866860..47868444,2	K562	blood:
3	chr3:47852912..47854715-chr3:47857178..47858993,2	K562	blood:
4	chr3:47851691..47863624-chr3:47863694..47870558,21	K562	blood:
5	chr3:47856299..47861442-chr3:47864746..47867839,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DHX30-1	chr3:47857453-47858462	NONHSAT089526

Variant related genes	Relation type
ENSG00000132153	Chromatin interaction

Extended variants
information (count: 170 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:168)

rs_ID	r²[population]
rs1013431	0.89[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap]
rs1060407	0.89[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.97[TSI][hapmap]
rs1061003	0.89[ASN][1000 genomes]
rs10865948	0.83[AMR][1000 genomes]
rs11130144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11130145	0.87[AMR][1000 genomes]
rs11130146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes]
rs11130147	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11130148	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11130150	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11130152	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1137524	0.85[ASN][1000 genomes]
rs11707679	0.89[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.97[TSI][hapmap]
rs11708849	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11710199	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11712464	1.00[CEU][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs11714942	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11716582	0.82[AMR][1000 genomes]
rs11927129	0.87[EUR][1000 genomes]
rs12492915	0.84[AMR][1000 genomes]
rs12495204	0.84[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12497921	0.86[AMR][1000 genomes]
rs12498027	0.86[AMR][1000 genomes]
rs12633604	0.85[AMR][1000 genomes]
rs12635438	1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.80[EUR][1000 genomes]
rs13061412	1.00[CEU][hapmap];0.92[AMR][1000 genomes]
rs13063042	1.00[CEU][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13064183	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13070035	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13074973	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13077230	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13079407	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13081356	0.87[AMR][1000 genomes]
rs13086149	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13091913	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13094264	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13098128	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1403578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes]
rs1403579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes]
rs1486915	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1684942	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17079785	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17290490	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs184388	0.83[ASN][1000 genomes]
rs2030596	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2047559	1.00[CEU][hapmap];0.84[AMR][1000 genomes]
rs2049301	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2101398	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2121754	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2133601	0.92[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes]
rs2140335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes]
rs2166770	0.89[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap]
rs2293226	0.82[AMR][1000 genomes]
rs2351248	0.82[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap]
rs2631721	0.88[ASN][1000 genomes]
rs2882611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes]
rs2882668	0.82[ASN][1000 genomes]
rs319682	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.87[ASN][1000 genomes]
rs319684	0.85[ASN][1000 genomes]
rs319685	0.85[ASN][1000 genomes]
rs319686	0.85[ASN][1000 genomes]
rs319689	0.85[ASN][1000 genomes]
rs319692	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs319693	1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs319694	0.84[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs319695	0.83[ASW][hapmap];0.89[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs319696	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs34025851	0.85[ASN][1000 genomes]
rs34249203	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34351471	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34569417	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34777284	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34906469	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35148469	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35582375	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35664069	0.80[EUR][1000 genomes]
rs35698005	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3732529	0.85[ASN][1000 genomes]
rs3755637	0.84[AMR][1000 genomes]
rs3755638	0.81[AMR][1000 genomes]
rs3772399	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772403	0.81[AMR][1000 genomes]
rs3915654	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4410463	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4858801	0.82[AMR][1000 genomes]
rs4858803	0.80[AMR][1000 genomes]
rs4858810	0.81[CEU][hapmap]
rs4858842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes]
rs4858846	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes]
rs4858851	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4858853	0.92[EUR][1000 genomes]
rs4858857	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4858860	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858863	1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4858871	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.85[ASN][1000 genomes]
rs55823596	0.90[EUR][1000 genomes]
rs56376646	0.87[EUR][1000 genomes]
rs60110914	0.82[AMR][1000 genomes]
rs60446735	0.85[ASN][1000 genomes]
rs61181421	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61620099	0.82[AMR][1000 genomes]
rs62262129	0.85[AMR][1000 genomes]
rs62263561	0.90[EUR][1000 genomes]
rs62263575	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6442072	0.86[AMR][1000 genomes]
rs6442074	0.86[AMR][1000 genomes]
rs6442079	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6442081	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6442082	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6442083	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6442085	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6442086	0.93[EUR][1000 genomes]
rs6763824	0.84[LWK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs6768699	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6772301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6772396	0.85[ASN][1000 genomes]
rs6773467	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6773732	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6774170	0.81[AMR][1000 genomes]
rs6776963	0.96[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs6777632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6782998	0.81[AMR][1000 genomes]
rs6783629	0.84[ASN][1000 genomes]
rs6785669	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6786001	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6792350	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6792497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6792737	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6806860	0.89[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72906488	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73085151	0.90[EUR][1000 genomes]
rs7374516	0.89[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.80[MKK][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap]
rs7426976	0.89[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap]
rs7427418	1.00[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];0.92[TSI][hapmap]
rs7429162	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7430879	0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]
rs7430913	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7612219	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7613934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes]
rs7618758	0.84[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7619882	0.82[ASN][1000 genomes]
rs7621236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes]
rs7624474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes]
rs7629850	1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7631950	0.82[AMR][1000 genomes]
rs7637372	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7637950	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7638103	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7645846	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7646982	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7649393	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7653368	0.82[ASN][1000 genomes]
rs777014	0.82[ASN][1000 genomes]
rs777015	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.85[ASN][1000 genomes]
rs796566	0.88[CEU][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs800762	0.87[ASN][1000 genomes]
rs810334	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.85[ASN][1000 genomes]
rs868255	0.82[AMR][1000 genomes]
rs870622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs883661	0.82[AMR][1000 genomes]
rs883662	1.00[CEU][hapmap];0.93[JPT][hapmap]
rs883663	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes]
rs9681917	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs9757517	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9812875	0.82[ASN][1000 genomes]
rs9842649	0.82[ASN][1000 genomes]
rs9850154	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9862913	0.89[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][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	nsv1003072	chr3:47673628-47869154	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv834679	chr3:47749475-47924006	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	167 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs3888	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs3888	ZNF589	cis	parietal	SCAN
rs3888	SMARCC1	cis	cerebellum	SCAN
rs3888	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs3888	HYAL2	cis	cerebellum	SCAN
rs3888	ZNF589	cis	cerebellum	SCAN
rs3888	MRPS18AP1	cis	Nerve Tibial	GTEx
rs3888	MRPS18AP1	cis	lung	GTEx
rs3888	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs3888	ZNF589	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47845600-47859000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:47845600-47866000	Weak transcription	Right Atrium	heart
3	chr3:47845600-47866200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:47845600-47866600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:47845800-47866000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:47846400-47863800	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr3:47846400-47865800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr3:47846600-47857600	Strong transcription	H1 Cell Line	embryonic stem cell
9	chr3:47846600-47858600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr3:47846600-47859200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr3:47846600-47863800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr3:47846600-47863800	Strong transcription	Fetal Thymus	thymus
13	chr3:47846600-47864000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr3:47846600-47864000	Strong transcription	Fetal Muscle Leg	muscle
15	chr3:47846600-47864200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:47846600-47864200	Strong transcription	Fetal Muscle Trunk	muscle
17	chr3:47846600-47865800	Weak transcription	Fetal Heart	heart
18	chr3:47846800-47863800	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr3:47846800-47864400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:47846800-47864600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:47846800-47864800	Strong transcription	Fetal Stomach	stomach
22	chr3:47846800-47865800	Weak transcription	Hela-S3	cervix
23	chr3:47847000-47862400	Strong transcription	Dnd41	blood
24	chr3:47847000-47864000	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr3:47847000-47864000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr3:47847400-47860600	Weak transcription	NHDF-Ad	bronchial
27	chr3:47848000-47863400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr3:47848200-47864000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr3:47848600-47861600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr3:47848600-47862400	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr3:47848600-47864000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr3:47848600-47864400	Strong transcription	Thymus	Thymus
33	chr3:47849600-47857600	Strong transcription	Brain Germinal Matrix	brain
34	chr3:47850800-47862400	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr3:47851200-47862600	Strong transcription	Primary B cells from peripheral blood	blood
36	chr3:47851200-47863800	Strong transcription	Stomach Smooth Muscle	stomach
37	chr3:47851600-47857600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr3:47851600-47862200	Strong transcription	Lung	lung
39	chr3:47852600-47866200	Weak transcription	Psoas Muscle	Psoas
40	chr3:47853000-47859400	Weak transcription	Pancreas	Pancrea
41	chr3:47853000-47859600	Weak transcription	Colonic Mucosa	Colon
42	chr3:47853000-47860000	Weak transcription	NHLF	lung
43	chr3:47853000-47860400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr3:47853000-47865800	Weak transcription	K562	blood
45	chr3:47853000-47866000	Weak transcription	Small Intestine	intestine
46	chr3:47853200-47858800	Weak transcription	HSMMtube	muscle
47	chr3:47853200-47859200	Weak transcription	Brain Substantia Nigra	brain
48	chr3:47853200-47860000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr3:47853200-47860400	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr3:47853200-47865800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links