Variant report

Variant	rs689884
Chromosome Location	chr15:52044258-52044259
allele	C/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	SIN3AK20	chr15:52043524-52044520	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr15:52041917-52044815	Raji	blood:	n/a	n/a
3	YY1	chr15:52043946-52044440	K562	blood:	n/a	chr15:52044196-52044207
4	POLR2A	chr15:52043195-52044362	GM18951	blood:	n/a	n/a
5	POLR2A	chr15:52044040-52044512	K562	blood:	n/a	n/a
6	POLR2A	chr15:52044135-52044448	GM12891	blood:	n/a	n/a
7	GTF2B	chr15:52044200-52044821	K562	blood:	n/a	n/a
8	UBTF	chr15:52043662-52044525	K562	blood:	n/a	n/a
9	MAX	chr15:52044230-52044840	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAX	chr15:52044184-52044844	NB4	blood:	n/a	n/a
11	GABPA	chr15:52043960-52044466	K562	blood:	n/a	chr15:52043998-52044007
12	POLR2A	chr15:52043133-52044543	GM19193	blood:	n/a	n/a
13	TAF7	chr15:52044234-52044408	K562	blood:	n/a	n/a
14	REST	chr15:52043122-52045074	H1-neurons	neurons:	n/a	chr15:52043960-52043970 chr15:52043874-52043892 chr15:52044155-52044168 chr15:52044199-52044212 chr15:52043965-52043978 chr15:52043838-52043851
15	MAX	chr15:52044191-52044798	H1-hESC	embryonic stem cell:	n/a	n/a
16	MAX	chr15:52043080-52044904	MCF-7	breast:	n/a	chr15:52043423-52043432 chr15:52043810-52043820
17	MAX	chr15:52044172-52044874	SK-N-SH	brain:	n/a	n/a
18	POLR2A	chr15:52044118-52044491	GM12891	blood:	n/a	n/a
19	MAX	chr15:52044134-52044598	ECC-1	luminal epithelium:	n/a	n/a
20	MAX	chr15:52043350-52044781	A549	lung:	n/a	chr15:52043423-52043432 chr15:52043810-52043820
21	HMGN3	chr15:52043441-52044409	K562	blood:	n/a	n/a
22	ZNF263	chr15:52043821-52044711	HEK293-T-REx	kidney:	n/a	n/a
23	POLR2A	chr15:52044048-52044468	K562	blood:	n/a	n/a
24	MAX	chr15:52044147-52044672	SK-N-SH	brain:	n/a	n/a
25	POLR2A	chr15:52043675-52044433	GM12892	blood:	n/a	n/a
26	SIN3AK20	chr15:52043918-52044512	K562	blood:	n/a	n/a
27	CCNT2	chr15:52043603-52044305	K562	blood:	n/a	chr15:52043685-52043694
28	HEY1	chr15:52044066-52044430	K562	blood:	n/a	n/a
29	MAX	chr15:52044139-52044687	A549	lung:	n/a	n/a
30	SIN3AK20	chr15:52044050-52044595	SK-N-SH	brain:	n/a	n/a
31	TBP	chr15:52044135-52044648	K562	blood:	n/a	n/a
32	POLR2A	chr15:52043877-52044518	K562	blood:	n/a	n/a
33	POLR2A	chr15:52043545-52044466	K562	blood:	n/a	n/a
34	POLR2A	chr15:52043185-52044418	GM15510	blood:	n/a	n/a
35	POLR2A	chr15:52044144-52044368	GM12878	blood:	n/a	n/a
36	HCFC1	chr15:52043337-52044412	K562	blood:	n/a	n/a
37	POLR2A	chr15:52044214-52044326	Gliobla	brain:	n/a	n/a
38	CHD2	chr15:52044205-52044420	K562	blood:	n/a	n/a
39	POLR2A	chr15:52043397-52044872	H1-neurons	neurons:	n/a	n/a
40	POLR2A	chr15:52043711-52044555	NB4	blood:	n/a	n/a
41	HEY1	chr15:52043668-52044491	K562	blood:	n/a	chr15:52043974-52043989 chr15:52043842-52043857 chr15:52043813-52043828 chr15:52043801-52043816
42	HA-E2F1	chr15:52043133-52044538	MCF-7	breast:	n/a	chr15:52043959-52043969 chr15:52043451-52043460
43	POLR2A	chr15:52043600-52044917	H1-neurons	neurons:	n/a	n/a
44	BHLHE40	chr15:52044227-52044396	K562	blood:	n/a	n/a
45	POLR2A	chr15:52044042-52044468	GM12892	blood:	n/a	n/a
46	MYC	chr15:52044252-52044805	NB4	blood:	n/a	n/a
47	UBTF	chr15:52043217-52044587	K562	blood:	n/a	n/a
48	E2F6	chr15:52043669-52044742	K562	blood:	n/a	chr15:52043959-52043969
49	SIN3A	chr15:52043214-52044723	H1-hESC	embryonic stem cell:	n/a	chr15:52044386-52044395
50	RCOR1	chr15:52044143-52044728	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:52028180..52031136-chr15:52040562..52045385,6	MCF-7	breast:
2	chr15:51913469..51917109-chr15:52042794..52045514,3	MCF-7	breast:
3	chr15:52029591..52032408-chr15:52042418..52044684,3	K562	blood:
4	chr15:52042996..52044811-chr15:52120947..52123164,2	MCF-7	breast:
5	chr15:52027363..52032665-chr15:52041435..52046045,23	MCF-7	breast:
6	chr15:52028355..52032748-chr15:52040539..52046492,10	K562	blood:

Variant related genes	Relation type
ENSG00000259377	TF binding region
LYSMD2	TF binding region
ENSG00000138594	Chromatin interaction
ENSG00000140280	Chromatin interaction
ENSG00000104093	Chromatin interaction

Extended variants
information (count: 169 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:167)

rs_ID	r²[population]
rs1001690	0.81[CHB][hapmap]
rs1035737	0.86[GIH][hapmap];0.85[TSI][hapmap]
rs10444798	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10444823	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10775145	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11049	0.87[CEU][hapmap]
rs11070864	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11070865	0.91[GIH][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes]
rs11070868	0.86[GIH][hapmap];0.85[TSI][hapmap]
rs1133882	0.88[CEU][hapmap]
rs11630084	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11630943	0.86[GIH][hapmap];0.85[TSI][hapmap]
rs11632106	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11636345	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11637876	0.86[GIH][hapmap];0.85[TSI][hapmap]
rs11638161	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11638766	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11638820	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12438686	0.86[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs12903707	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12905283	0.86[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes]
rs12908327	0.86[GIH][hapmap];0.85[TSI][hapmap]
rs12917133	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1350174	0.96[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1466276	0.84[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1545602	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17526463	0.86[GIH][hapmap];0.85[TSI][hapmap]
rs17526760	0.86[GIH][hapmap];0.85[TSI][hapmap]
rs17611193	0.86[GIH][hapmap];0.85[TSI][hapmap]
rs17705732	0.90[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs1811326	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1840708	0.86[GIH][hapmap];0.87[TSI][hapmap]
rs1867984	0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1895863	0.82[ASN][1000 genomes]
rs1902430	0.96[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1972689	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2006772	0.87[EUR][1000 genomes]
rs2007355	0.89[GIH][hapmap];0.85[TSI][hapmap]
rs2009972	0.86[CHB][hapmap];0.91[CHD][hapmap]
rs2014638	0.92[CEU][hapmap];0.93[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs2034856	0.89[GIH][hapmap];0.83[MKK][hapmap];0.85[TSI][hapmap]
rs2034857	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2034858	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2052709	0.90[CHB][hapmap]
rs2077743	0.92[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2114191	0.81[GIH][hapmap];0.85[TSI][hapmap]
rs2252606	0.95[CHB][hapmap]
rs2252831	0.89[GIH][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap]
rs2253116	0.95[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap]
rs2264339	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2303443	0.92[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs2414116	0.93[GIH][hapmap];0.88[MKK][hapmap]
rs2414117	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2414119	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2414122	0.81[GIH][hapmap]
rs2433217	0.83[GIH][hapmap];0.83[TSI][hapmap]
rs2433221	0.84[GIH][hapmap];0.85[TSI][hapmap]
rs2436660	0.84[GIH][hapmap];0.85[TSI][hapmap]
rs2436661	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2441780	0.86[GIH][hapmap];0.85[TSI][hapmap]
rs2448946	0.84[GIH][hapmap];0.85[TSI][hapmap]
rs2448953	0.81[CEU][hapmap]
rs2470612	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs2470619	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2554305	0.91[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2554306	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2554307	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2554308	0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2554315	0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs2554327	0.89[GIH][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap]
rs2554332	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs2554334	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2554336	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2554345	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2554349	0.90[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap]
rs2570224	0.92[CEU][hapmap];0.95[GIH][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs2570228	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2570231	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2570233	0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2570235	0.88[EUR][1000 genomes]
rs2570236	0.86[EUR][1000 genomes]
rs2570237	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2570238	0.81[AMR][1000 genomes]
rs2570239	0.89[GIH][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap]
rs2570241	0.89[GIH][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap]
rs2570251	0.87[EUR][1000 genomes]
rs2570252	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs2570253	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs2570258	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2570260	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2593170	0.86[GIH][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap]
rs2593173	0.95[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap]
rs2593191	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2593202	0.95[CHB][hapmap]
rs2623254	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2623259	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs2623262	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2623271	0.89[GIH][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap]
rs2623281	0.95[CHB][hapmap]
rs2623283	0.95[CHB][hapmap]
rs2912189	0.86[GIH][hapmap];0.83[TSI][hapmap]
rs2916169	0.81[CEU][hapmap]
rs2916172	0.86[GIH][hapmap];0.85[TSI][hapmap]
rs2916176	0.86[GIH][hapmap];0.85[TSI][hapmap]
rs2916177	0.84[GIH][hapmap];0.85[TSI][hapmap]
rs2929425	0.86[GIH][hapmap];0.85[TSI][hapmap]
rs2929426	0.84[GIH][hapmap];0.85[TSI][hapmap]
rs2959285	0.86[GIH][hapmap];0.85[TSI][hapmap]
rs2959298	0.81[GIH][hapmap];0.85[TSI][hapmap]
rs2959299	0.84[GIH][hapmap];0.85[TSI][hapmap]
rs3088312	0.84[AMR][1000 genomes]
rs3751596	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3794530	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3794534	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3794535	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3794536	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4238383	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4502160	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4534783	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4622456	0.92[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4774602	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4775978	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4775982	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4775983	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55843525	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55887408	0.89[EUR][1000 genomes]
rs58758283	0.86[ASN][1000 genomes]
rs60329909	0.86[ASN][1000 genomes]
rs6493515	0.85[EUR][1000 genomes]
rs6493518	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6493519	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6493520	0.86[GIH][hapmap];0.85[TSI][hapmap]
rs6493522	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6493523	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6493525	0.86[GIH][hapmap];0.85[TSI][hapmap]
rs6493526	0.84[GIH][hapmap];0.85[TSI][hapmap]
rs67895020	0.83[EUR][1000 genomes]
rs689922	0.94[ASN][1000 genomes]
rs690287	0.93[ASN][1000 genomes]
rs690638	0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs7163176	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7165283	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs7165585	0.92[CEU][hapmap];0.88[GIH][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7166110	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7166962	0.87[AMR][1000 genomes]
rs7168659	0.81[CHB][hapmap];0.87[AMR][1000 genomes]
rs7171459	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7173375	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7174497	0.86[GIH][hapmap];0.87[TSI][hapmap]
rs7174808	0.86[GIH][hapmap];0.87[TSI][hapmap]
rs7174941	0.89[EUR][1000 genomes]
rs7176421	0.83[ASN][1000 genomes]
rs7181553	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7182917	0.86[EUR][1000 genomes]
rs72732952	0.81[ASN][1000 genomes]
rs8024081	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8024088	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8024589	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8026521	0.91[AMR][1000 genomes]
rs8027721	0.85[AMR][1000 genomes]
rs8028258	0.92[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8028890	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8028922	0.86[GIH][hapmap];0.85[TSI][hapmap]
rs8035173	0.88[GIH][hapmap]
rs8041268	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs919059	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9635308	0.95[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]

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	esv2830011	chr15:52027777-52048710	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a
2	nsv569409	chr15:52028914-52268144	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs689884	SCG3	cis	Temporal Cortex	GTEx
rs689884	SCG3	cis	Cerebellum	GTEx
rs689884	SCG3	cis	Frontal Cortex	GTEx
rs689884	SCG3	cis	cerebellum	SCAN
rs689884	SCG3	cis	Brain Pons	GTEx
rs689884	LYSMD2	cis	Muscle Skeletal	GTEx
rs689884	TMOD2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52042800-52044600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
2	chr15:52042800-52044600	Active TSS	Brain Anterior Caudate	brain
3	chr15:52042800-52044800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr15:52043000-52044400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
5	chr15:52043000-52044600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
6	chr15:52043000-52044600	Active TSS	Brain Substantia Nigra	brain
7	chr15:52043000-52044600	Active TSS	Rectal Smooth Muscle	rectum
8	chr15:52043000-52044800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
9	chr15:52043000-52044800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
10	chr15:52043000-52045200	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr15:52043200-52044400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr15:52043200-52044400	Active TSS	Duodenum Mucosa	Duodenum
13	chr15:52043200-52044400	Bivalent/Poised TSS	A549	lung
14	chr15:52043200-52044600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr15:52043200-52044600	Active TSS	H9 Cell Line	embryonic stem cell
16	chr15:52043200-52044600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr15:52043200-52044600	Active TSS	Aorta	Aorta
18	chr15:52043200-52044600	Active TSS	Esophagus	oesophagus
19	chr15:52043200-52044600	Active TSS	Fetal Intestine Large	intestine
20	chr15:52043200-52044600	Active TSS	Right Ventricle	heart
21	chr15:52043200-52044600	Bivalent/Poised TSS	Hela-S3	cervix
22	chr15:52043200-52044600	Bivalent/Poised TSS	HSMM	muscle
23	chr15:52043200-52044800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr15:52043200-52044800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr15:52043200-52044800	Active TSS	Psoas Muscle	Psoas
26	chr15:52043200-52045200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
27	chr15:52043400-52044400	Active TSS	Primary T cells from cord blood	blood
28	chr15:52043400-52044400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr15:52043400-52044400	Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr15:52043400-52044400	Active TSS	Gastric	stomach
31	chr15:52043400-52044400	Active TSS	Placenta Amnion	Placenta Amnion
32	chr15:52043400-52044400	Active TSS	Rectal Mucosa Donor 29	rectum
33	chr15:52043400-52044400	Active TSS	Sigmoid Colon	Sigmoid Colon
34	chr15:52043400-52044400	Active TSS	Small Intestine	intestine
35	chr15:52043400-52044400	Bivalent/Poised TSS	HepG2	liver
36	chr15:52043400-52044600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr15:52043400-52044600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
38	chr15:52043400-52044600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr15:52043400-52044600	Active TSS	Brain Hippocampus Middle	brain
40	chr15:52043400-52044600	Active TSS	Colon Smooth Muscle	Colon
41	chr15:52043400-52044600	Active TSS	Fetal Intestine Small	intestine
42	chr15:52043400-52044600	Active TSS	Left Ventricle	heart
43	chr15:52043400-52044600	Active TSS	NHLF	lung
44	chr15:52043400-52044800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
45	chr15:52043400-52044800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr15:52043400-52044800	Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr15:52043400-52045000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr15:52043400-52045000	Active TSS	Brain Angular Gyrus	brain
49	chr15:52043400-52045000	Active TSS	Fetal Brain Female	brain
50	chr15:52043400-52045200	Active TSS	Brain Cingulate Gyrus	brain

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Variant report

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