Variant report

Variant	rs1133415
Chromosome Location	chr3:52575831-52575832
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52574434..52577960-chr3:52578839..52582098,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NT5DC2-1	chr3:52573952-52575907	ENSG00000245797

Extended variants
information (count: 192 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:187)

rs_ID	r²[population]
rs1010552	0.84[CHB][hapmap]
rs1010553	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs1010554	0.91[CHB][hapmap];0.86[CHD][hapmap]
rs10510760	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10780035	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs10865973	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs10865974	0.91[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap]
rs1108842	0.91[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap]
rs11130307	0.83[ASN][1000 genomes]
rs11130308	0.84[ASN][1000 genomes]
rs11130310	0.91[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap]
rs11130311	0.81[ASN][1000 genomes]
rs11130312	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11130313	0.82[ASN][1000 genomes]
rs11130314	0.81[ASN][1000 genomes]
rs11130315	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.81[ASN][1000 genomes]
rs11130317	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap]
rs11130323	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs11177	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs11235	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs11708075	0.85[ASN][1000 genomes]
rs11709284	0.93[ASN][1000 genomes]
rs11709448	0.82[ASN][1000 genomes]
rs11711421	0.96[CEU][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11714419	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[ASN][1000 genomes]
rs11714565	0.88[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11716747	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs11717043	0.83[ASN][1000 genomes]
rs11718420	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11718509	0.84[ASN][1000 genomes]
rs11720159	0.91[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs11720243	0.91[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.81[ASN][1000 genomes]
rs11720432	0.83[ASN][1000 genomes]
rs12486847	0.81[ASN][1000 genomes]
rs12487445	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.83[ASN][1000 genomes]
rs12487591	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.83[ASN][1000 genomes]
rs12488461	0.86[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap]
rs12489732	0.98[ASN][1000 genomes]
rs12489828	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs12496634	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap]
rs12498066	0.84[ASN][1000 genomes]
rs12629699	0.81[ASN][1000 genomes]
rs12629701	0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12632381	0.83[ASN][1000 genomes]
rs12635140	0.91[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap]
rs13059862	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13060048	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13060675	0.81[ASN][1000 genomes]
rs13063160	0.86[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13064064	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.83[ASN][1000 genomes]
rs13065019	0.82[ASN][1000 genomes]
rs13065851	0.82[ASN][1000 genomes]
rs13068293	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.83[ASN][1000 genomes]
rs13069481	0.82[ASN][1000 genomes]
rs13076398	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13079063	0.90[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap]
rs13081028	0.86[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.82[ASN][1000 genomes]
rs13081031	0.82[ASN][1000 genomes]
rs13083798	0.91[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap]
rs13085331	0.84[ASN][1000 genomes]
rs13085775	0.86[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.88[TSI][hapmap];0.82[ASN][1000 genomes]
rs13085895	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs13086297	0.82[ASN][1000 genomes]
rs13086898	0.81[ASN][1000 genomes]
rs13303	0.95[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs13621	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1561337	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.83[ASN][1000 genomes]
rs1570	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17052256	0.88[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17052259	0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17264436	0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1821879	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1866268	0.91[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap]
rs1961958	0.86[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.94[ASN][1000 genomes]
rs1961959	0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2015971	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs2028216	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.80[ASN][1000 genomes]
rs2079929	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap]
rs2083180	0.91[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.82[ASN][1000 genomes]
rs2118540	0.89[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs2159644	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs2164884	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.84[ASN][1000 genomes]
rs2164885	0.90[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap]
rs2251219	0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2268027	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2276824	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs2289247	0.91[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap]
rs2289249	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.98[ASN][1000 genomes]
rs2289250	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.82[ASN][1000 genomes]
rs2336145	0.83[ASN][1000 genomes]
rs2336146	0.91[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.84[ASN][1000 genomes]
rs2336149	0.91[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.81[ASN][1000 genomes]
rs2577831	0.91[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap]
rs2590838	0.91[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap]
rs2590846	0.81[ASN][1000 genomes]
rs28661185	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2878628	0.88[ASW][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs33964154	0.99[ASN][1000 genomes]
rs33967311	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.82[ASN][1000 genomes]
rs34005367	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34017441	0.91[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs34115864	0.85[ASN][1000 genomes]
rs34173654	0.83[ASN][1000 genomes]
rs34215106	0.83[ASN][1000 genomes]
rs34341238	0.80[ASN][1000 genomes]
rs34537256	0.83[ASN][1000 genomes]
rs34754793	0.84[ASN][1000 genomes]
rs34757451	0.82[ASN][1000 genomes]
rs34954168	0.85[ASN][1000 genomes]
rs35107891	0.84[ASN][1000 genomes]
rs35211965	0.82[ASN][1000 genomes]
rs35249778	0.83[ASN][1000 genomes]
rs35409678	0.80[ASN][1000 genomes]
rs35526119	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap]
rs35976524	0.81[ASN][1000 genomes]
rs3733039	0.91[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap]
rs3733041	0.91[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap]
rs3733045	0.91[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.83[ASN][1000 genomes]
rs3755798	0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap]
rs3755806	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.83[ASN][1000 genomes]
rs3774365	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3774366	0.91[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.83[ASN][1000 genomes]
rs3796353	0.88[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3852066	0.91[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.84[ASN][1000 genomes]
rs4234633	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4282054	0.95[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs4434138	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4475032	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4687546	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4687547	0.85[ASN][1000 genomes]
rs4687548	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4687624	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4687625	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4687626	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4687629	0.80[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4687630	0.81[ASN][1000 genomes]
rs4687633	0.84[ASN][1000 genomes]
rs4687636	0.86[TSI][hapmap];0.83[ASN][1000 genomes]
rs4687637	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4687638	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.82[ASN][1000 genomes]
rs4687639	0.83[ASN][1000 genomes]
rs62253700	0.85[ASN][1000 genomes]
rs62253703	0.83[ASN][1000 genomes]
rs62253733	0.82[ASN][1000 genomes]
rs62255362	0.81[ASN][1000 genomes]
rs62256903	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6445528	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445529	0.82[ASN][1000 genomes]
rs6445534	0.80[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs6445535	0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap]
rs6617	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs66782572	0.82[ASN][1000 genomes]
rs6762457	0.85[ASN][1000 genomes]
rs6762813	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs6768697	0.81[ASN][1000 genomes]
rs6770463	0.81[ASN][1000 genomes]
rs6778735	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.90[ASN][1000 genomes]
rs6778844	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.98[ASN][1000 genomes]
rs6786043	0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.94[ASN][1000 genomes]
rs6786919	0.88[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6788887	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6788993	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6790330	0.83[ASN][1000 genomes]
rs6796726	0.81[ASN][1000 genomes]
rs6798246	0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs68021750	0.85[ASN][1000 genomes]
rs6804145	0.91[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.81[ASN][1000 genomes]
rs6805156	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6976	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs731831	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs7611731	0.91[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.81[ASN][1000 genomes]
rs7614498	0.83[ASN][1000 genomes]
rs7614981	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs7622694	0.91[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.82[ASN][1000 genomes]
rs7623199	0.85[ASN][1000 genomes]
rs7624716	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap]
rs7625743	0.85[ASN][1000 genomes]
rs7628578	0.84[ASN][1000 genomes]
rs7636227	0.91[ASN][1000 genomes]
rs7638808	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7652191	0.91[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.85[ASN][1000 genomes]
rs767418	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap]
rs8906	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs9758945	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9853056	0.86[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap]
rs9879090	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs9917834	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv876793	chr3:52450043-52584787	Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs1133415	GLYCTK	cis	parietal	SCAN
rs1133415	ITIH4	cis	parietal	SCAN
rs1133415	SPCS1	cis	parietal	SCAN
rs1133415	GNL3	cis	cerebellum	SCAN
rs1133415	NEK4	cis	parietal	SCAN
rs1133415	NEK4	cis	cerebellum	SCAN
rs1133415	MUSTN1	cis	Artery Aorta	GTEx
rs1133415	TMEM110	cis	parietal	SCAN
rs1133415	RBM6	cis	cerebellum	SCAN
rs1133415	NISCH	cis	parietal	SCAN
rs1133415	GLT8D1	Cis_1M	lymphoblastoid	RTeQTL
rs1133415	NT5DC2	cis	multi-tissue	Pritchard
rs1133415	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs1133415	NT5DC2	cis	Lymphoblastoid	GTEx
rs1133415	GNL3	cis	parietal	SCAN
rs1133415	NT5DC2	cis	lymphoblastoid	seeQTL
rs1133415	TMEM110	cis	cerebellum	SCAN
rs1133415	GLT8D1	cis	lymphoblastoid	seeQTL
rs1133415	NT5DC2	cis	Skin Sun Exposed Lower leg	GTEx
rs1133415	RBM6	cis	parietal	SCAN
rs1133415	FLJ12442	cis	multi-tissue	Pritchard
rs1133415	PBRM1	cis	Thyroid	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52571400-52594200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:52572200-52581000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:52572200-52584400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:52572400-52578800	Weak transcription	A549	lung
5	chr3:52572400-52580600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:52572400-52581800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:52572400-52594200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:52572400-52633000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:52573200-52576200	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr3:52573200-52576400	Strong transcription	Fetal Muscle Trunk	muscle
11	chr3:52573200-52576600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:52573200-52578600	Weak transcription	Brain Germinal Matrix	brain
13	chr3:52573200-52579000	Weak transcription	Thymus	Thymus
14	chr3:52573200-52582000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr3:52573200-52583400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr3:52573200-52585000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:52573200-52586400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:52573200-52589600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr3:52573200-52590400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:52573400-52576000	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr3:52573400-52576000	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr3:52573400-52576200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:52573400-52576200	Strong transcription	NHLF	lung
24	chr3:52573400-52580600	Weak transcription	Fetal Brain Male	brain
25	chr3:52573400-52585200	Weak transcription	Small Intestine	intestine
26	chr3:52573400-52595000	Weak transcription	Stomach Mucosa	stomach
27	chr3:52573600-52576000	Strong transcription	Duodenum Mucosa	Duodenum
28	chr3:52573600-52576000	Strong transcription	HSMM	muscle
29	chr3:52573600-52576200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:52573600-52576200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:52573600-52576200	Strong transcription	Fetal Muscle Leg	muscle
32	chr3:52573600-52576400	Strong transcription	NHEK	skin
33	chr3:52573600-52577600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:52573600-52578400	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr3:52573600-52578600	Weak transcription	Aorta	Aorta
36	chr3:52573600-52578800	Weak transcription	Brain Hippocampus Middle	brain
37	chr3:52573600-52578800	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr3:52573600-52578800	Weak transcription	Fetal Brain Female	brain
39	chr3:52573600-52580600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr3:52573600-52580600	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr3:52573600-52581200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr3:52573600-52581200	Weak transcription	Esophagus	oesophagus
43	chr3:52573600-52582000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr3:52573600-52582000	Weak transcription	Ovary	ovary
45	chr3:52573600-52583200	Weak transcription	Colonic Mucosa	Colon
46	chr3:52573600-52598400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr3:52573800-52579000	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr3:52573800-52584600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr3:52574000-52576000	Strong transcription	Placenta	Placenta
50	chr3:52574000-52576000	Strong transcription	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links