Variant report

Variant	rs2232248
Chromosome Location	chr3:50609624-50609625
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ELK1	chr3:50609601-50609817	K562	blood:	n/a	n/a
2	CTCF	chr3:50609527-50609853	MCF-7	breast:	n/a	chr3:50609713-50609726 chr3:50609712-50609733 chr3:50609710-50609728 chr3:50609711-50609727 chr3:50609649-50609658 chr3:50609713-50609722
3	CTCF	chr3:50609496-50609866	MCF-7	breast:	n/a	chr3:50609713-50609726 chr3:50609712-50609733 chr3:50609710-50609728 chr3:50609711-50609727 chr3:50609649-50609658 chr3:50609713-50609722
4	CTCF	chr3:50609498-50609932	GM12878	blood:	n/a	chr3:50609713-50609726 chr3:50609712-50609733 chr3:50609710-50609728 chr3:50609711-50609727 chr3:50609649-50609658 chr3:50609713-50609722
5	SMC3	chr3:50609543-50609929	Hela-S3	cervix:	n/a	chr3:50609712-50609726 chr3:50609648-50609655 chr3:50609716-50609726
6	RCOR1	chr3:50609585-50609825	HepG2	liver:	n/a	n/a
7	CTCF	chr3:50609563-50609840	Fibrobl	skin:	n/a	chr3:50609713-50609726 chr3:50609712-50609733 chr3:50609710-50609728 chr3:50609711-50609727 chr3:50609649-50609658 chr3:50609713-50609722
8	YY1	chr3:50609576-50609939	HepG2	liver:	n/a	n/a
9	NFIC	chr3:50609608-50609928	HepG2	liver:	n/a	n/a
10	MYC	chr3:50609599-50609821	K562	blood:	n/a	n/a
11	TBL1XR1	chr3:50609613-50609894	K562	blood:	n/a	n/a
12	CTCF	chr3:50609598-50609800	A549	lung:	n/a	chr3:50609713-50609726 chr3:50609712-50609733 chr3:50609710-50609728 chr3:50609711-50609727 chr3:50609649-50609658 chr3:50609713-50609722
13	GTF2F1	chr3:50609619-50609875	K562	blood:	n/a	n/a
14	RAD21	chr3:50609494-50609978	SK-N-SH_RA	brain:	n/a	chr3:50609716-50609726 chr3:50609711-50609730 chr3:50609716-50609728
15	CTCF	chr3:50609620-50609770	HEK293	kidney:	n/a	chr3:50609713-50609726 chr3:50609712-50609733 chr3:50609710-50609728 chr3:50609711-50609727 chr3:50609649-50609658 chr3:50609713-50609722
16	CTCF	chr3:50609575-50609849	A549	lung:	n/a	chr3:50609713-50609726 chr3:50609712-50609733 chr3:50609710-50609728 chr3:50609711-50609727 chr3:50609649-50609658 chr3:50609713-50609722
17	CTCF	chr3:50609620-50609770	GM12874	blood:	n/a	chr3:50609713-50609726 chr3:50609712-50609733 chr3:50609710-50609728 chr3:50609711-50609727 chr3:50609649-50609658 chr3:50609713-50609722
18	CTCF	chr3:50609474-50609936	H1-hESC	embryonic stem cell:	n/a	chr3:50609713-50609726 chr3:50609712-50609733 chr3:50609710-50609728 chr3:50609711-50609727 chr3:50609649-50609658 chr3:50609713-50609722
19	CTCF	chr3:50609405-50609866	GM12891	blood:	n/a	chr3:50609713-50609726 chr3:50609712-50609733 chr3:50609710-50609728 chr3:50609711-50609727 chr3:50609649-50609658 chr3:50609713-50609722
20	USF2	chr3:50609582-50609828	Hela-S3	cervix:	n/a	n/a
21	CTCF	chr3:50609609-50609831	GM10248	blood:	n/a	chr3:50609713-50609726 chr3:50609712-50609733 chr3:50609710-50609728 chr3:50609711-50609727 chr3:50609649-50609658 chr3:50609713-50609722
22	CTCF	chr3:50609290-50610749	SK-N-SH	brain:	n/a	chr3:50609713-50609726 chr3:50609712-50609733 chr3:50609710-50609728 chr3:50609711-50609727 chr3:50609649-50609658 chr3:50609713-50609722
23	CTCF	chr3:50609505-50609959	IMR90	lung:	n/a	chr3:50609713-50609726 chr3:50609712-50609733 chr3:50609710-50609728 chr3:50609711-50609727 chr3:50609649-50609658 chr3:50609713-50609722
24	MYC	chr3:50609565-50609765	MCF10A-Er-Src	breast:	n/a	n/a
25	RAD21	chr3:50609534-50609910	K562	blood:	n/a	chr3:50609716-50609726 chr3:50609711-50609730 chr3:50609716-50609728
26	ZNF143	chr3:50609575-50609869	K562	blood:	n/a	n/a
27	RAD21	chr3:50609372-50610215	HCT-116	colon:	n/a	chr3:50609716-50609726 chr3:50609711-50609730 chr3:50609716-50609728
28	CTCF	chr3:50609576-50609847	Hela-S3	cervix:	n/a	chr3:50609713-50609726 chr3:50609712-50609733 chr3:50609710-50609728 chr3:50609711-50609727 chr3:50609649-50609658 chr3:50609713-50609722
29	RAD21	chr3:50609531-50609975	HepG2	liver:	n/a	chr3:50609716-50609726 chr3:50609711-50609730 chr3:50609716-50609728
30	CTCF	chr3:50609540-50609886	ECC-1	luminal epithelium:	n/a	chr3:50609713-50609726 chr3:50609712-50609733 chr3:50609710-50609728 chr3:50609711-50609727 chr3:50609649-50609658 chr3:50609713-50609722
31	CTCF	chr3:50609540-50609883	GM12892	blood:	n/a	chr3:50609713-50609726 chr3:50609712-50609733 chr3:50609710-50609728 chr3:50609711-50609727 chr3:50609649-50609658 chr3:50609713-50609722
32	CTCF	chr3:50609608-50609797	SK-N-SH_RA	brain:	n/a	chr3:50609713-50609726 chr3:50609712-50609733 chr3:50609710-50609728 chr3:50609711-50609727 chr3:50609649-50609658 chr3:50609713-50609722
33	SIN3AK20	chr3:50609564-50609887	SK-N-SH	brain:	n/a	n/a
34	CTCF	chr3:50609463-50610010	MCF-7	breast:	n/a	chr3:50609713-50609726 chr3:50609712-50609733 chr3:50609710-50609728 chr3:50609711-50609727 chr3:50609649-50609658 chr3:50609713-50609722
35	STAT5A	chr3:50609456-50610076	GM12878	blood:	n/a	chr3:50609655-50609667 chr3:50609660-50609668
36	CTCF	chr3:50609583-50609810	A549	lung:	n/a	chr3:50609713-50609726 chr3:50609712-50609733 chr3:50609710-50609728 chr3:50609711-50609727 chr3:50609649-50609658 chr3:50609713-50609722
37	CTCF	chr3:50609545-50609837	MCF-7	breast:	n/a	chr3:50609713-50609726 chr3:50609712-50609733 chr3:50609710-50609728 chr3:50609711-50609727 chr3:50609649-50609658 chr3:50609713-50609722
38	CTCF	chr3:50609620-50609770	GM12868	blood:	n/a	chr3:50609713-50609726 chr3:50609712-50609733 chr3:50609710-50609728 chr3:50609711-50609727 chr3:50609649-50609658 chr3:50609713-50609722
39	CTCF	chr3:50609524-50609896	K562	blood:	n/a	chr3:50609713-50609726 chr3:50609712-50609733 chr3:50609710-50609728 chr3:50609711-50609727 chr3:50609649-50609658 chr3:50609713-50609722
40	CTCF	chr3:50609595-50609861	SK-N-SH_RA	brain:	n/a	chr3:50609713-50609726 chr3:50609712-50609733 chr3:50609710-50609728 chr3:50609711-50609727 chr3:50609649-50609658 chr3:50609713-50609722
41	RAD21	chr3:50609551-50609878	GM12878	blood:	n/a	chr3:50609716-50609726 chr3:50609711-50609730 chr3:50609716-50609728
42	RAD21	chr3:50609525-50609984	IMR90	lung:	n/a	chr3:50609716-50609726 chr3:50609711-50609730 chr3:50609716-50609728
43	RAD21	chr3:50609426-50610046	ECC-1	luminal epithelium:	n/a	chr3:50609716-50609726 chr3:50609711-50609730 chr3:50609716-50609728
44	FOXM1	chr3:50609474-50609898	GM12878	blood:	n/a	n/a
45	CTCF	chr3:50609600-50609750	GM12873	blood:	n/a	chr3:50609713-50609726 chr3:50609712-50609733 chr3:50609710-50609728 chr3:50609711-50609727 chr3:50609649-50609658 chr3:50609713-50609722
46	CTCF	chr3:50609620-50609770	GM12866	blood:	n/a	chr3:50609713-50609726 chr3:50609712-50609733 chr3:50609710-50609728 chr3:50609711-50609727 chr3:50609649-50609658 chr3:50609713-50609722
47	CTCF	chr3:50609620-50609770	HCT-116	colon:	n/a	chr3:50609713-50609726 chr3:50609712-50609733 chr3:50609710-50609728 chr3:50609711-50609727 chr3:50609649-50609658 chr3:50609713-50609722
48	CTCF	chr3:50609620-50609770	NB4	blood:	n/a	chr3:50609713-50609726 chr3:50609712-50609733 chr3:50609710-50609728 chr3:50609711-50609727 chr3:50609649-50609658 chr3:50609713-50609722
49	CTCF	chr3:50609596-50609835	GM13977	blood:	n/a	chr3:50609713-50609726 chr3:50609712-50609733 chr3:50609710-50609728 chr3:50609711-50609727 chr3:50609649-50609658 chr3:50609713-50609722
50	CTCF	chr3:50609404-50610125	HCT-116	colon:	n/a	chr3:50609713-50609726 chr3:50609712-50609733 chr3:50609710-50609728 chr3:50609711-50609727 chr3:50609649-50609658 chr3:50609713-50609722

No.	Distal block	Cell Line	Cell type
1	chr3:50608421..50610660-chr3:51421926..51423993,2	K562	blood:
2	chr3:50588788..50589450-chr3:50609431..50610085,3	MCF-7	breast:
3	chr3:50606526..50611586-chr3:50612274..50616724,6	MCF-7	breast:
4	chr3:50609228..50610208-chr3:50651239..50652218,7	MCF-7	breast:
5	chr3:50609273..50610196-chr3:50653035..50654024,2	K562	blood:
6	chr3:50599337..50613537-chr3:50634306..50660129,118	MCF-7	breast:
7	chr3:50609496..50610096-chr3:50689886..50690548,2	MCF-7	breast:
8	chr3:50607017..50612379-chr3:51423330..51426962,5	MCF-7	breast:
9	chr3:50609170..50610450-chr3:50649619..50652186,24	K562	blood:
10	chr3:50607067..50609858-chr3:50721017..50723839,2	K562	blood:
11	chr3:50608156..50612219-chr3:50612794..50616407,4	K562	blood:
12	chr3:50601756..50613871-chr3:50647072..50654542,28	K562	blood:
13	chr3:50609237..50610758-chr3:50651130..50652154,11	MCF-7	breast:
14	chr3:50605586..50608239-chr3:50609168..50611221,2	MCF-7	breast:
15	chr3:50603678..50606671-chr3:50607262..50609999,2	K562	blood:

Variant related genes	Relation type
C3orf18	TF binding region
HEMK1	TF binding region
ENSG00000114735	Chromatin interaction
ENSG00000114737	Chromatin interaction
ENSG00000228337	Chromatin interaction
ENSG00000088543	Chromatin interaction
ENSG00000114738	Chromatin interaction
ENSG00000145050	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs1013233	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1034405	1.00[CEU][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs11130252	0.85[EUR][1000 genomes]
rs11712367	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap]
rs11716398	0.80[AMR][1000 genomes]
rs11719998	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12491425	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12493985	0.88[EUR][1000 genomes]
rs12639126	0.80[CEU][hapmap]
rs129310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13076850	0.90[EUR][1000 genomes]
rs13083004	0.90[EUR][1000 genomes]
rs13084476	0.85[EUR][1000 genomes]
rs13091933	0.94[CEU][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs13094336	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs1385025	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs175634	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17787569	1.00[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs1824281	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1971976	0.82[AMR][1000 genomes]
rs201193	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs201194	0.94[CEU][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs201196	0.90[EUR][1000 genomes]
rs201198	1.00[CEU][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs2227280	0.91[EUR][1000 genomes]
rs2232253	0.91[EUR][1000 genomes]
rs2269505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2269507	0.91[EUR][1000 genomes]
rs2355321	0.91[EUR][1000 genomes]
rs2355323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2608988	0.86[TSI][hapmap]
rs2609024	0.86[TSI][hapmap]
rs2675773	0.87[CEU][hapmap]
rs2675810	0.86[TSI][hapmap]
rs34202063	0.91[EUR][1000 genomes]
rs34267788	0.82[EUR][1000 genomes]
rs34399912	0.91[EUR][1000 genomes]
rs34434811	0.82[EUR][1000 genomes]
rs34584636	1.00[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs34756253	0.85[EUR][1000 genomes]
rs34848480	0.82[AMR][1000 genomes]
rs34889917	0.91[EUR][1000 genomes]
rs35655236	0.90[EUR][1000 genomes]
rs35690191	0.90[EUR][1000 genomes]
rs35714264	0.86[EUR][1000 genomes]
rs35864641	0.82[EUR][1000 genomes]
rs375544	1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3792325	0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3792328	1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3804627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3804632	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs391620	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3943212	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes]
rs396302	0.95[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.84[ASN][1000 genomes]
rs398703	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs399484	1.00[CEU][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs399971	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs414171	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs417592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs441516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs443030	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs443436	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs448028	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4485709	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap]
rs4533647	0.82[EUR][1000 genomes]
rs453570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688712	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs490634	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs59949730	0.91[EUR][1000 genomes]
rs616589	0.90[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs628081	0.94[CEU][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6446212	1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap]
rs6446213	1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap]
rs67588094	0.91[EUR][1000 genomes]
rs6778680	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6779819	1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes]
rs67813889	0.93[EUR][1000 genomes]
rs6784166	0.86[EUR][1000 genomes]
rs6787521	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs6791880	0.86[TSI][hapmap]
rs6796769	1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs695170	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71326937	0.91[EUR][1000 genomes]
rs728901	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes]
rs750453	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs750510	0.89[CEU][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs751851	0.82[AMR][1000 genomes]
rs754298	0.81[CHD][hapmap];0.82[MEX][hapmap];0.81[EUR][1000 genomes]
rs7615703	1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs7635666	0.80[AMR][1000 genomes]
rs7646236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs808149	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs809454	0.86[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs813243	1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs900735	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9682401	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9825535	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap]
rs9826757	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs9830920	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription 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	103 gene(s)	inside rSNPs	diseases
3	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription 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	104 gene(s)	inside rSNPs	diseases
4	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv432419	chr3:50388396-50637496	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv1013225	chr3:50440826-50700448	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv536566	chr3:50440826-50700448	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv984540	chr3:50473691-50669310	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
9	nsv1012501	chr3:50483037-50679591	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	nsv536567	chr3:50483037-50679591	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
11	nsv460532	chr3:50536273-50616049	Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases
12	nsv590272	chr3:50536273-50616049	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases
13	nsv460533	chr3:50574213-50678151	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
14	nsv590273	chr3:50574213-50678151	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2232248	HEMK1	cis	Lymphoblastoid	GTEx
rs2232248	HEMK1	cis	cerebellum	SCAN
rs2232248	MST1	cis	cerebellum	SCAN
rs2232248	HEMK	cis	multi-tissue	Pritchard
rs2232248	MAPKAPK3	cis	multi-tissue	Pritchard
rs2232248	ALS2CL	cis	parietal	SCAN
rs2232248	HEMK1	cis	lymphoblastoid	seeQTL
rs2232248	HEMK1	cis	parietal	SCAN
rs2232248	APEH	cis	cerebellum	SCAN
rs2232248	HEMK1	cis	multi-tissue	Pritchard

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50607400-50615600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr3:50607400-50628200	Weak transcription	Small Intestine	intestine
3	chr3:50607600-50609800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr3:50607600-50609800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr3:50607600-50609800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr3:50607600-50609800	Weak transcription	Left Ventricle	heart
7	chr3:50607600-50609800	Weak transcription	Lung	lung
8	chr3:50607600-50609800	Weak transcription	Stomach Mucosa	stomach
9	chr3:50607600-50610400	Enhancers	Primary T cells from cord blood	blood
10	chr3:50607600-50613000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:50607600-50614400	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr3:50607600-50617600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:50607600-50628400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:50607800-50609800	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr3:50607800-50609800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr3:50607800-50609800	Enhancers	Fetal Intestine Large	intestine
17	chr3:50607800-50609800	Enhancers	Fetal Thymus	thymus
18	chr3:50607800-50609800	Weak transcription	Psoas Muscle	Psoas
19	chr3:50607800-50609800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr3:50607800-50610600	Enhancers	Duodenum Mucosa	Duodenum
21	chr3:50607800-50611800	Enhancers	Liver	Liver
22	chr3:50607800-50612000	Weak transcription	Ovary	ovary
23	chr3:50607800-50614200	Weak transcription	Brain Anterior Caudate	brain
24	chr3:50607800-50614800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr3:50607800-50615200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr3:50607800-50615200	Weak transcription	Aorta	Aorta
27	chr3:50607800-50620000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:50607800-50628200	Weak transcription	HSMMtube	muscle
29	chr3:50607800-50628600	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr3:50608000-50609800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr3:50608000-50609800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr3:50608000-50609800	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr3:50608000-50609800	Weak transcription	Fetal Heart	heart
34	chr3:50608000-50609800	Weak transcription	Thymus	Thymus
35	chr3:50608000-50609800	Enhancers	HepG2	liver
36	chr3:50608000-50609800	Enhancers	K562	blood
37	chr3:50608000-50610200	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr3:50608000-50610200	Genic enhancers	Fetal Stomach	stomach
39	chr3:50608000-50610200	Weak transcription	HSMM	muscle
40	chr3:50608000-50610800	Weak transcription	Brain Angular Gyrus	brain
41	chr3:50608000-50610800	Transcr. at gene 5' and 3'	Dnd41	blood
42	chr3:50608000-50611000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr3:50608000-50613000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr3:50608000-50618400	Weak transcription	NH-A	brain
45	chr3:50608000-50621400	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr3:50608000-50621400	Weak transcription	HUVEC	blood vessel
47	chr3:50608000-50621800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr3:50608200-50609800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:50608200-50609800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:50608200-50609800	Weak transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links