Variant report

Variant	rs296888
Chromosome Location	chr9:86595498-86595499
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	POLR2A	chr9:86593844-86596744	H1-hESC	embryonic stem cell:	n/a	n/a
2	CREB1	chr9:86594278-86595948	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr9:86593922-86596698	K562	blood:	n/a	n/a
4	POLR2A	chr9:86594364-86595834	A549	lung:	n/a	n/a
5	JUND	chr9:86595354-86595775	H1-hESC	embryonic stem cell:	n/a	n/a
6	PBX3	chr9:86594236-86596215	SK-N-SH	brain:	n/a	chr9:86595226-86595246
7	ELK1	chr9:86594922-86595687	K562	blood:	n/a	n/a
8	E2F6	chr9:86595009-86595940	A549	lung:	n/a	chr9:86595043-86595052 chr9:86595620-86595632 chr9:86595094-86595103 chr9:86595270-86595279 chr9:86595620-86595629 chr9:86595696-86595708 chr9:86595621-86595636
9	SP1	chr9:86594287-86596067	A549	lung:	n/a	chr9:86595268-86595280 chr9:86595270-86595279 chr9:86595147-86595161 chr9:86595871-86595881 chr9:86595871-86595880 chr9:86595621-86595630 chr9:86594928-86594937 chr9:86594434-86594448 chr9:86594595-86594609 chr9:86595620-86595629 chr9:86594434-86594443 chr9:86595547-86595561 chr9:86594927-86594939 chr9:86594737-86594746 chr9:86595872-86595881 chr9:86595871-86595880 chr9:86594596-86594605 chr9:86595665-86595679 chr9:86595550-86595562 chr9:86595616-86595630 chr9:86595872-86595885 chr9:86595142-86595151 chr9:86595551-86595560 chr9:86595552-86595561 chr9:86595269-86595278 chr9:86595269-86595279 chr9:86594430-86594439 chr9:86595621-86595630 chr9:86595551-86595561 chr9:86595550-86595562 chr9:86594435-86594444 chr9:86594924-86594938 chr9:86595619-86595631 chr9:86595140-86595152 chr9:86594594-86594606 chr9:86595269-86595283
10	TEAD4	chr9:86595148-86595696	HepG2	liver:	n/a	n/a
11	POLR2A	chr9:86593958-86596248	K562	blood:	n/a	n/a
12	ZBTB33	chr9:86594835-86595922	A549	lung:	n/a	chr9:86595579-86595589 chr9:86595576-86595591 chr9:86595578-86595587
13	YY1	chr9:86594278-86595907	K562	blood:	n/a	chr9:86595086-86595097 chr9:86594539-86594549 chr9:86594914-86594924 chr9:86594533-86594550 chr9:86595094-86595103 chr9:86595620-86595629 chr9:86595140-86595151
14	IRF1	chr9:86594272-86595912	K562	blood:	n/a	chr9:86594484-86594495 chr9:86594483-86594495 chr9:86594484-86594498 chr9:86595182-86595191 chr9:86594431-86594445 chr9:86595619-86595633 chr9:86594480-86594494
15	PML	chr9:86594292-86596039	K562	blood:	n/a	n/a
16	CEBPB	chr9:86595435-86595836	K562	blood:	n/a	n/a
17	CEBPD	chr9:86594857-86595930	K562	blood:	n/a	n/a
18	POLR2A	chr9:86593110-86595750	A549	lung:	n/a	n/a
19	ZKSCAN1	chr9:86594769-86596644	Hela-S3	cervix:	n/a	n/a
20	SPI1	chr9:86595439-86595948	GM12891	blood:	n/a	chr9:86595616-86595629 chr9:86595621-86595634
21	MXI1	chr9:86595104-86595898	H1-hESC	embryonic stem cell:	n/a	n/a
22	ATF1	chr9:86594482-86595795	K562	blood:	n/a	n/a
23	YY1	chr9:86595472-86595587	K562	blood:	n/a	n/a
24	MXI1	chr9:86593619-86596557	Hela-S3	cervix:	n/a	n/a
25	MAX	chr9:86594290-86595872	HUVEC	blood vessel:	n/a	chr9:86594612-86594619 chr9:86595614-86595624 chr9:86595618-86595628
26	HEY1	chr9:86593873-86596014	HepG2	liver:	n/a	chr9:86595085-86595100 chr9:86595677-86595692
27	POLR2A	chr9:86594111-86596658	ECC-1	luminal epithelium:	n/a	n/a
28	POLR2A	chr9:86593061-86596929	SK-N-MC	brain:	n/a	n/a
29	MAX	chr9:86593949-86596953	A549	lung:	n/a	chr9:86594612-86594619 chr9:86595614-86595624 chr9:86595618-86595628
30	E2F6	chr9:86594954-86596106	K562	blood:	n/a	chr9:86595043-86595052 chr9:86595620-86595632 chr9:86595094-86595103 chr9:86595270-86595279 chr9:86595620-86595629 chr9:86595696-86595708 chr9:86595621-86595636
31	POU2F2	chr9:86594783-86595726	GM12878	blood:	n/a	chr9:86595270-86595282 chr9:86595617-86595629 chr9:86594922-86594934 chr9:86595547-86595559
32	EGR1	chr9:86595394-86595675	GM12878	blood:	n/a	chr9:86595615-86595628 chr9:86595614-86595629 chr9:86595615-86595628 chr9:86595617-86595627
33	ATF2	chr9:86594095-86595833	H1-hESC	embryonic stem cell:	n/a	n/a
34	FOXM1	chr9:86594256-86595997	GM12878	blood:	n/a	n/a
35	ZBTB33	chr9:86595354-86595759	K562	blood:	n/a	chr9:86595579-86595589 chr9:86595576-86595591 chr9:86595578-86595587
36	BCL3	chr9:86594199-86595879	A549	lung:	n/a	chr9:86595732-86595741 chr9:86595085-86595094 chr9:86594760-86594769 chr9:86595086-86595099
37	SIN3AK20	chr9:86595256-86595976	A549	lung:	n/a	n/a
38	MAX	chr9:86594346-86596530	SK-N-SH	brain:	n/a	chr9:86594612-86594619 chr9:86595614-86595624 chr9:86595618-86595628
39	POLR2A	chr9:86594012-86596039	PFSK-1	brain:	n/a	n/a
40	POLR2A	chr9:86593882-86596480	GM12891	blood:	n/a	n/a
41	TCF12	chr9:86594247-86596222	MCF-7	breast:	n/a	chr9:86596024-86596031 chr9:86594510-86594517 chr9:86596020-86596030
42	TAF1	chr9:86594143-86596210	A549	lung:	n/a	n/a
43	PBX3	chr9:86594197-86596105	SK-N-SH	brain:	n/a	chr9:86595226-86595246
44	RFX5	chr9:86595235-86595693	K562	blood:	n/a	n/a
45	RAD21	chr9:86595427-86595855	SK-N-SH_RA	brain:	n/a	chr9:86595547-86595557
46	RELA	chr9:86594040-86596640	GM18951	blood:	n/a	n/a
47	REST	chr9:86595216-86595821	K562	blood:	n/a	chr9:86595761-86595774
48	ZBTB33	chr9:86594986-86595817	HepG2	liver:	n/a	chr9:86595579-86595589 chr9:86595576-86595591 chr9:86595578-86595587
49	SP2	chr9:86594891-86595530	HepG2	liver:	n/a	chr9:86595225-86595248 chr9:86595146-86595161
50	TAF1	chr9:86594801-86595814	GM12891	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr9:86595452-86595502	SKMC	muscle:	n/a
2	chr9:86595452-86595502	HMEC	breast:	n/a
3	chr9:86595452-86595502	AG10803	skin:	n/a
4	chr9:86595452-86595502	NHBE	bronchial:	n/a
5	chr9:86595452-86595502	AG04450	lung:	fetal
6	chr9:86595452-86595502	HCPEpiC	choroid plexus:	n/a
7	chr9:86595452-86595502	RPTEC	kidney:	n/a
8	chr9:86595452-86595502	IMR90	lung:	fetal
9	chr9:86595452-86595502	HEK293	kidney:	embryo
10	chr9:86595452-86595502	SK-N-SH	brain:	n/a
11	chr9:86595452-86595502	HEEpiC	esophagus:	n/a
12	chr9:86595452-86595502	MCF-7	breast:	n/a
13	chr9:86595452-86595502	HRE	kidney:	n/a
14	chr9:86595452-86595502	AG04449	skin:	fetal
15	chr9:86595452-86595502	Caco-2	colon:	n/a
16	chr9:86595452-86595502	Hela-S3	cervix:	n/a
17	chr9:86595452-86595502	HepG2	liver:	n/a
18	chr9:86595452-86595502	HCT-116	colon:	n/a
19	chr9:86595452-86595502	CMK	blood:	n/a
20	chr9:86595452-86595502	Jurkat	blood:	n/a
21	chr9:86595452-86595502	BE2_C	brain:	n/a
22	chr9:86595452-86595502	GM12891	blood:	n/a
23	chr9:86595452-86595502	HL-60	blood:	n/a
24	chr9:86595452-86595502	NT2-D1	testis:	n/a
25	chr9:86595452-86595502	GM12878	blood:	n/a
26	chr9:86595452-86595502	HCM	heart:	n/a
27	chr9:86595452-86595502	AG09309	skin:	n/a
28	chr9:86595452-86595502	SK-N-MC	brain:	n/a
29	chr9:86595452-86595502	NH-A	brain:	n/a
30	chr9:86595452-86595502	ProgFib	skin:	n/a
31	chr9:86595452-86595502	U87	brain:	n/a
32	chr9:86595452-86595502	MCF10A-Er-Src	breast:	n/a
33	chr9:86595452-86595502	K562	blood:	n/a
34	chr9:86595452-86595502	NB4	blood:	n/a
35	chr9:86595452-86595502	HAEpiC	amniotic membrane:	n/a
36	chr9:86595452-86595502	GM12892	blood:	n/a
37	chr9:86595452-86595502	PFSK-1	brain:	n/a
38	chr9:86595452-86595502	GM19239	blood:	n/a
39	chr9:86595452-86595502	PANC-1	pancreas:	n/a
40	chr9:86595452-86595502	SK-N-SH_RA	brain:	n/a
41	chr9:86595452-86595502	Hepatocyte	liver:	n/a
42	chr9:86595452-86595502	LNCaP	prostate:	n/a
43	chr9:86595452-86595502	HUVEC	blood vessel:	n/a
44	chr9:86595452-86595502	H1-hESC	embryonic stem cell:	embryo
45	chr9:86595452-86595502	BJ	skin:	n/a
46	chr9:86595452-86595502	HNPCEpiC	eye:	n/a
47	chr9:86595452-86595502	ECC-1	luminal epithelium:	n/a
48	chr9:86595452-86595502	HRPEpiC	eye:	n/a
49	chr9:86595452-86595502	AG09319	gingival:	n/a
50	chr9:86595452-86595502	HCF	heart:	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:86533979..86537502-chr9:86594012..86596999,11	MCF-7	breast:
2	chr2:203129679..203130563-chr9:86595056..86595797,2	Hela-S3	cervix:
3	chr17:34890789..34891390-chr9:86595392..86595894,2	Hela-S3	cervix:
4	chr16:776639..778399-chr9:86594223..86596178,2	MCF-7	breast:
5	chr11:18655371..18656340-chr9:86595063..86595728,2	NB4	blood:
6	chr6:33359301..33359882-chr9:86594730..86595587,2	Hela-S3	cervix:
7	chr12:7052976..7053657-chr9:86594802..86595608,2	Hela-S3	cervix:
8	chr5:133560806..133561386-chr9:86594639..86595588,2	Hela-S3	cervix:
9	chr18:12376849..12377806-chr9:86594670..86595620,2	Hela-S3	cervix:
10	chr9:86320289..86324589-chr9:86593742..86599530,6	K562	blood:
11	chr9:86533593..86537892-chr9:86593047..86598677,10	K562	blood:
12	chr15:66796716..66797533-chr9:86595214..86595851,2	Hela-S3	cervix:
13	chr3:184080676..184081504-chr9:86595141..86595996,2	NB4	blood:
14	chr9:86319810..86324349-chr9:86592631..86598226,6	K562	blood:
15	chr11:94799931..94800625-chr9:86595070..86595772,2	Hela-S3	cervix:
16	chr9:86594678..86596625-chr9:86954974..86956986,2	MCF-7	breast:
17	chr20:56964201..56965088-chr9:86595330..86595831,2	Hela-S3	cervix:
18	chr15:75940235..75940930-chr9:86595138..86596000,2	Hela-S3	cervix:
19	chr9:86534520..86537940-chr9:86592614..86595774,6	K562	blood:
20	chr22:29196469..29197140-chr9:86595287..86595817,2	Hela-S3	cervix:
21	chr19:49228274..49229018-chr9:86595338..86596004,2	Hela-S3	cervix:
22	chr7:138794412..138795161-chr9:86594899..86595728,2	NB4	blood:
23	chr9:86593375..86596264-chr9:101558546..101560057,2	MCF-7	breast:
24	chr3:14988158..14990908-chr9:86594139..86596513,2	MCF-7	breast:
25	chr12:46766121..46766688-chr9:86595377..86596150,2	Hela-S3	cervix:
26	chr9:86592736..86597542-chr9:86606160..86610925,6	K562	blood:
27	chr8:53372582..53373541-chr9:86594741..86595608,2	Hela-S3	cervix:
28	chr9:86593982..86596635-chr9:88968626..88970254,2	MCF-7	breast:
29	chr9:86533247..86537973-chr9:86593370..86597981,20	MCF-7	breast:
30	chr3:170587539..170588434-chr9:86594849..86595680,2	Hela-S3	cervix:
31	chr7:104652758..104653646-chr9:86595375..86596036,2	HCT-116	colon:
32	chr10:90639734..90640291-chr9:86595257..86596036,2	Hela-S3	cervix:
33	chr11:62609023..62610551-chr9:86593862..86596703,2	MCF-7	breast:

Variant related genes	Relation type
RMI1	TF binding region
HNRNPK	TF binding region
RMI1	CpG island
HNRNPK	CpG island
ENSG00000147488	Chromatin interaction
ENSG00000202523	Chromatin interaction
ENSG00000113575	Chromatin interaction
ENSG00000103253	Chromatin interaction
ENSG00000163882	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000225733	Chromatin interaction
ENSG00000197506	Chromatin interaction
ENSG00000177971	Chromatin interaction
ENSG00000179119	Chromatin interaction
ENSG00000174442	Chromatin interaction
ENSG00000184886	Chromatin interaction
ENSG00000162004	Chromatin interaction
ENSG00000100219	Chromatin interaction
ENSG00000228393	Chromatin interaction
ENSG00000165115	Chromatin interaction
ENSG00000138134	Chromatin interaction
ENSG00000254473	Chromatin interaction
ENSG00000124164	Chromatin interaction
ENSG00000134294	Chromatin interaction
ENSG00000173548	Chromatin interaction
ENSG00000083223	Chromatin interaction
ENSG00000135018	Chromatin interaction
ENSG00000055044	Chromatin interaction
ENSG00000226471	Chromatin interaction
ENSG00000177463	Chromatin interaction
ENSG00000141385	Chromatin interaction
ENSG00000163584	Chromatin interaction
ENSG00000238923	Chromatin interaction
ENSG00000141140	Chromatin interaction
ENSG00000174444	Chromatin interaction
ENSG00000111678	Chromatin interaction
ENSG00000165138	Chromatin interaction
ENSG00000271885	Chromatin interaction
ENSG00000237649	Chromatin interaction
ENSG00000105939	Chromatin interaction
ENSG00000180771	Chromatin interaction
ENSG00000105538	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10114889	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10115699	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10125715	0.82[ASN][1000 genomes]
rs10868068	0.81[EUR][1000 genomes]
rs10868070	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10868071	0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10868076	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10868080	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11140251	0.82[CHB][hapmap]
rs11140253	0.82[CHB][hapmap]
rs11140265	0.88[CHB][hapmap];0.92[JPT][hapmap]
rs11140289	0.83[EUR][1000 genomes]
rs11140304	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12378956	0.87[CHB][hapmap];0.92[JPT][hapmap]
rs12682981	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs13290882	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap]
rs13296528	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs167203	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs1831757	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[EUR][1000 genomes]
rs1889113	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1982151	0.89[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2576362	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2780103	1.00[ASW][hapmap];0.82[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs296883	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs296886	0.87[CEU][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs296887	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs296889	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs296890	0.94[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs296892	0.86[YRI][hapmap]
rs296893	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs296894	0.81[CEU][hapmap]
rs3180887	0.82[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap]
rs3818725	0.82[CHB][hapmap];0.86[ASN][1000 genomes]
rs4147132	1.00[ASW][hapmap];0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.86[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4147133	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4535826	0.94[ASW][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.83[MKK][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4877814	0.86[YRI][hapmap]
rs4877815	0.82[YRI][hapmap]
rs6559742	0.81[CEU][hapmap]
rs6559751	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6559752	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6559753	0.86[YRI][hapmap]
rs6559756	0.86[YRI][hapmap]
rs696825	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7020300	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7021189	0.86[YRI][hapmap]
rs7033292	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs7045126	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7853254	0.86[EUR][1000 genomes]
rs7853377	0.87[CEU][hapmap]
rs7869321	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs7875011	0.86[YRI][hapmap]
rs796003	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs796004	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs796007	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs930340	0.80[CEU][hapmap]
rs9410888	0.82[CHB][hapmap]
rs963459	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758192	chr9:86414024-86603602	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	esv2759701	chr9:86414024-86603602	Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
3	nsv831644	chr9:86534310-86704395	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
4	esv3366490	chr9:86541369-86608868	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
5	nsv1043703	chr9:86545917-86603545	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
6	nsv893514	chr9:86584160-86678917	Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs296888	LOC440173	cis	parietal	SCAN
rs296888	C9orf64	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86591600-86596600	Active TSS	Ovary	ovary
2	chr9:86591800-86597000	Active TSS	Psoas Muscle	Psoas
3	chr9:86592200-86596800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr9:86592200-86597000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr9:86592400-86596200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
6	chr9:86592400-86596400	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr9:86592400-86596600	Active TSS	Aorta	Aorta
8	chr9:86592400-86596800	Active TSS	Right Ventricle	heart
9	chr9:86592400-86597600	Active TSS	Fetal Brain Female	brain
10	chr9:86592600-86596200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr9:86592600-86596400	Active TSS	HSMMtube	muscle
12	chr9:86592600-86596600	Active TSS	Cortex derived primary cultured neurospheres	brain
13	chr9:86592600-86596600	Active TSS	Thymus	Thymus
14	chr9:86592600-86596800	Active TSS	Right Atrium	heart
15	chr9:86592600-86597000	Active TSS	Stomach Smooth Muscle	stomach
16	chr9:86592800-86596400	Active TSS	Fetal Muscle Leg	muscle
17	chr9:86592800-86596400	Active TSS	Placenta Amnion	Placenta Amnion
18	chr9:86592800-86596400	Active TSS	HMEC	breast
19	chr9:86592800-86596600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
20	chr9:86592800-86596600	Active TSS	Fetal Intestine Large	intestine
21	chr9:86592800-86596600	Active TSS	Fetal Intestine Small	intestine
22	chr9:86592800-86596800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr9:86592800-86597200	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr9:86592800-86597200	Active TSS	NHLF	lung
25	chr9:86593000-86596200	Active TSS	Skeletal Muscle Female	skeletal muscle
26	chr9:86593000-86596400	Active TSS	Primary T helper naive cells from peripheral blood	blood
27	chr9:86593000-86596400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr9:86593000-86596400	Active TSS	Brain Angular Gyrus	brain
29	chr9:86593000-86596400	Active TSS	Brain Anterior Caudate	brain
30	chr9:86593000-86596400	Active TSS	Brain Cingulate Gyrus	brain
31	chr9:86593000-86596400	Active TSS	Brain Hippocampus Middle	brain
32	chr9:86593000-86596400	Active TSS	Colon Smooth Muscle	Colon
33	chr9:86593000-86596400	Active TSS	Fetal Stomach	stomach
34	chr9:86593000-86596400	Active TSS	Rectal Mucosa Donor 31	rectum
35	chr9:86593000-86596400	Active TSS	Rectal Smooth Muscle	rectum
36	chr9:86593000-86596400	Active TSS	Hela-S3	cervix
37	chr9:86593000-86596400	Active TSS	HUVEC	blood vessel
38	chr9:86593000-86596400	Active TSS	NH-A	brain
39	chr9:86593000-86596600	Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr9:86593000-86596600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr9:86593000-86596600	Active TSS	Duodenum Mucosa	Duodenum
42	chr9:86593000-86596600	Active TSS	Fetal Kidney	kidney
43	chr9:86593000-86596800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
44	chr9:86593000-86596800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr9:86593000-86596800	Active TSS	Fetal Thymus	thymus
46	chr9:86593000-86596800	Active TSS	HSMM	muscle
47	chr9:86593000-86596800	Active TSS	NHDF-Ad	bronchial
48	chr9:86593000-86597000	Active TSS	H9 Cell Line	embryonic stem cell
49	chr9:86593000-86597000	Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr9:86593000-86597200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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