Variant report

Variant	rs998909
Chromosome Location	chr3:52805093-52805094
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:424)
CpG islands
(count:122)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:424 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F6	chr3:52804813-52805285	A549	lung:	n/a	n/a
2	TAF1	chr3:52804643-52805354	SK-N-SH	brain:	n/a	n/a
3	CTCF	chr3:52804980-52805130	HCPEpiC	choroid plexus:	n/a	chr3:52805000-52805013
4	POLR2A	chr3:52804702-52805482	MCF10A-Er-Src	breast:	n/a	n/a
5	CHD2	chr3:52805088-52805243	K562	blood:	n/a	n/a
6	POLR2A	chr3:52804398-52805652	Hela-S3	cervix:	n/a	n/a
7	MAX	chr3:52804664-52805438	SK-N-SH	brain:	n/a	n/a
8	SIN3AK20	chr3:52804436-52805220	H1-hESC	embryonic stem cell:	n/a	n/a
9	TAF1	chr3:52804592-52805422	A549	lung:	n/a	n/a
10	STAT5A	chr3:52804842-52805623	GM12878	blood:	n/a	n/a
11	CTCF	chr3:52804960-52805110	HPF	lung:	n/a	chr3:52805000-52805013
12	IRF1	chr3:52804787-52805506	K562	blood:	n/a	n/a
13	GABPA	chr3:52804824-52805382	MCF-7	breast:	n/a	chr3:52804953-52804967 chr3:52804905-52804914 chr3:52804956-52804967
14	MYC	chr3:52804588-52805120	MCF-7	breast:	n/a	n/a
15	CTCF	chr3:52804960-52805110	HPAF	blood vessel:	n/a	chr3:52805000-52805013
16	POLR2A	chr3:52804674-52805403	SK-N-SH	brain:	n/a	n/a
17	POLR2A	chr3:52804640-52805334	K562	blood:	n/a	n/a
18	ETS1	chr3:52804691-52805286	K562	blood:	n/a	n/a
19	SP1	chr3:52804824-52805266	H1-hESC	embryonic stem cell:	n/a	n/a
20	SP4	chr3:52804577-52805404	H1-hESC	embryonic stem cell:	n/a	chr3:52804629-52804645
21	MYC	chr3:52804844-52805259	H1-hESC	embryonic stem cell:	n/a	n/a
22	MAX	chr3:52804770-52805336	HepG2	liver:	n/a	n/a
23	POLR2A	chr3:52804866-52805560	HL-60	blood:	n/a	n/a
24	SIN3AK20	chr3:52804998-52805236	H1-hESC	embryonic stem cell:	n/a	n/a
25	MAX	chr3:52804866-52805205	K562	blood:	n/a	n/a
26	FOXA2	chr3:52805011-52805396	HepG2	liver:	n/a	n/a
27	FOXP2	chr3:52804783-52805176	PFSK-1	brain:	n/a	n/a
28	REST	chr3:52804944-52805204	PANC-1	pancreas:	n/a	n/a
29	POLR2A	chr3:52804555-52805429	U87	brain:	n/a	n/a
30	SP1	chr3:52804785-52805358	A549	lung:	n/a	n/a
31	YY1	chr3:52804643-52805259	H1-hESC	embryonic stem cell:	n/a	chr3:52804794-52804805
32	FOSL2	chr3:52804954-52805434	A549	lung:	n/a	n/a
33	TBL1XR1	chr3:52804899-52805362	K562	blood:	n/a	n/a
34	REST	chr3:52804813-52805282	A549	lung:	n/a	n/a
35	ARID3A	chr3:52805013-52805335	K562	blood:	n/a	n/a
36	POLR2A	chr3:52804525-52805377	GM18951	blood:	n/a	n/a
37	EP300	chr3:52805050-52805250	HepG2	liver:	n/a	n/a
38	POLR2A	chr3:52804665-52805361	GM19193	blood:	n/a	n/a
39	WRNIP1	chr3:52805009-52805626	GM12878	blood:	n/a	n/a
40	MYC	chr3:52804844-52805478	MCF10A-Er-Src	breast:	n/a	n/a
41	POLR2A	chr3:52804619-52805308	HepG2	liver:	n/a	n/a
42	TAF1	chr3:52804718-52805322	K562	blood:	n/a	n/a
43	USF2	chr3:52804988-52805354	HepG2	liver:	n/a	n/a
44	POLR2A	chr3:52804643-52805233	HepG2	liver:	n/a	n/a
45	POLR2A	chr3:52804667-52805485	GM12878	blood:	n/a	n/a
46	TEAD4	chr3:52804934-52805405	HepG2	liver:	n/a	n/a
47	ATF3	chr3:52804938-52805185	K562	blood:	n/a	n/a
48	RAD21	chr3:52804712-52805250	IMR90	lung:	n/a	chr3:52804999-52805013
49	POLR2A	chr3:52804602-52805531	K562	blood:	n/a	n/a
50	TAF1	chr3:52804503-52805466	ECC-1	luminal epithelium:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:52805078-52805128	CMK	blood:	n/a
2	chr3:52805078-52805128	PFSK-1	brain:	n/a
3	chr3:52805078-52805128	NB4	blood:	n/a
4	chr3:52805078-52805128	NHBE	bronchial:	n/a
5	chr3:52805072-52805122	AG04450	lung:	fetal
6	chr3:52805078-52805128	HAEpiC	amniotic membrane:	n/a
7	chr3:52805072-52805122	MCF10A-Er-Src	breast:	n/a
8	chr3:52805072-52805122	MCF-7	breast:	n/a
9	chr3:52805078-52805128	HCT-116	colon:	n/a
10	chr3:52805072-52805122	AG09319	gingival:	n/a
11	chr3:52805078-52805128	HEEpiC	esophagus:	n/a
12	chr3:52805078-52805128	MCF-7	breast:	n/a
13	chr3:52805072-52805122	HIPEpiC	eye:	n/a
14	chr3:52805078-52805128	MCF10A-Er-Src	breast:	n/a
15	chr3:52805078-52805128	K562	blood:	n/a
16	chr3:52805072-52805122	A549	lung:	n/a
17	chr3:52805078-52805128	HRCEpiC	kidney:	n/a
18	chr3:52805072-52805122	Hela-S3	cervix:	n/a
19	chr3:52805078-52805128	Jurkat	blood:	n/a
20	chr3:52805078-52805128	GM06990	blood:	n/a
21	chr3:52805072-52805122	HEEpiC	esophagus:	n/a
22	chr3:52805072-52805122	HRCEpiC	kidney:	n/a
23	chr3:52805072-52805122	HNPCEpiC	eye:	n/a
24	chr3:52805078-52805128	AG09309	skin:	n/a
25	chr3:52805078-52805128	Caco-2	colon:	n/a
26	chr3:52805078-52805128	A549	lung:	n/a
27	chr3:52805078-52805128	SK-N-SH	brain:	n/a
28	chr3:52805072-52805122	HL-60	blood:	n/a
29	chr3:52805078-52805128	HRE	kidney:	n/a
30	chr3:52805078-52805128	ECC-1	luminal epithelium:	n/a
31	chr3:52805072-52805122	K562	blood:	n/a
32	chr3:52805072-52805122	NHBE	bronchial:	n/a
33	chr3:52805078-52805128	HPAEpiC	pulmonary alveolar:	n/a
34	chr3:52805078-52805128	HMEC	breast:	n/a
35	chr3:52805078-52805128	SK-N-MC	brain:	n/a
36	chr3:52805078-52805128	PrEC	prostate:	n/a
37	chr3:52805078-52805128	IMR90	lung:	fetal
38	chr3:52805078-52805128	PANC-1	pancreas:	n/a
39	chr3:52805072-52805122	HUVEC	blood vessel:	n/a
40	chr3:52805078-52805128	NHDF-neo	bronchial:	n/a
41	chr3:52805072-52805122	NB4	blood:	n/a
42	chr3:52805072-52805122	Caco-2	colon:	n/a
43	chr3:52805078-52805128	LNCaP	prostate:	n/a
44	chr3:52805078-52805128	T-47D	breast:	n/a
45	chr3:52805072-52805122	Jurkat	blood:	n/a
46	chr3:52805078-52805128	HCF	heart:	n/a
47	chr3:52805072-52805122	NT2-D1	testis:	n/a
48	chr3:52805078-52805128	SK-N-SH_RA	brain:	n/a
49	chr3:52805072-52805122	HRPEpiC	eye:	n/a
50	chr3:52805072-52805122	HRE	kidney:	n/a

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52804713..52805559-chr7:25164453..25165216,2	HCT-116	colon:
2	chr3:52442610..52445343-chr3:52803282..52805357,2	K562	blood:
3	chr3:52804965..52807932-chr3:52819198..52822291,3	K562	blood:
4	chr3:52804965..52807719-chr3:52819198..52820979,2	K562	blood:
5	chr3:52803948..52806345-chr3:52865313..52866850,2	MCF-7	breast:
6	chr3:52804845..52806455-chr3:52854968..52857676,2	MCF-7	breast:
7	chr3:52803280..52805303-chr3:52832255..52833885,2	MCF-7	breast:
8	chr3:52719292..52721392-chr3:52805038..52806656,2	K562	blood:
9	chr3:52803715..52805902-chr3:52874029..52875964,2	MCF-7	breast:
10	chr3:52802780..52807602-chr3:52827391..52831755,5	K562	blood:
11	chr3:52766545..52769494-chr3:52804406..52806680,2	K562	blood:
12	chr3:52722798..52726345-chr3:52803116..52806448,3	K562	blood:

No data

Variant related genes	Relation type
NEK4	TF binding region
NEK4	CpG island
ENSG00000172115	Chromatin interaction
ENSG00000055955	Chromatin interaction
ENSG00000213533	Chromatin interaction
ENSG00000055957	Chromatin interaction
ENSG00000248592	Chromatin interaction
ENSG00000212493	Chromatin interaction
ENSG00000270941	Chromatin interaction
ENSG00000238862	Chromatin interaction
ENSG00000163939	Chromatin interaction
ENSG00000163938	Chromatin interaction
ENSG00000162267	Chromatin interaction
ENSG00000010318	Chromatin interaction
ENSG00000163930	Chromatin interaction
ENSG00000222345	Chromatin interaction
ENSG00000252787	Chromatin interaction

Extended variants
information (count: 225 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:220)

rs_ID	r²[population]
rs1014969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1029871	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1042779	0.82[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10510760	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1075653	0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs1076425	0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs10780035	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10865973	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10865974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1108842	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs11130308	0.86[EUR][1000 genomes]
rs11130310	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11130311	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11130312	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11130313	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11130314	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11130315	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11130317	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11130319	0.85[ASN][1000 genomes]
rs11130321	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11130323	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11130324	0.89[ASN][1000 genomes]
rs11130325	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11130326	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11130327	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11177	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11235	0.95[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs11708075	0.81[EUR][1000 genomes]
rs11709448	0.81[ASN][1000 genomes]
rs11714030	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11714088	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11714419	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs11714565	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs11716747	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11717043	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11717836	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11718420	0.84[EUR][1000 genomes]
rs11718509	0.81[EUR][1000 genomes]
rs11720159	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs11720243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs11720432	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12486554	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12486847	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12487445	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12487591	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12488461	0.91[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12496476	0.82[EUR][1000 genomes]
rs12496634	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12497998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12498066	0.82[EUR][1000 genomes]
rs12629699	0.80[EUR][1000 genomes]
rs12629701	0.84[EUR][1000 genomes]
rs12632265	0.85[ASN][1000 genomes]
rs12635140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13060675	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13061253	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13061423	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13064064	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13065019	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13065851	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13068293	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13069481	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13071584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13074853	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13076193	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13079063	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13081031	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13082208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13082960	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13083798	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs13085331	0.82[EUR][1000 genomes]
rs13085775	0.84[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13085895	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13086297	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13086898	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13087772	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13095332	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1468638	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1561337	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17264436	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1866268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2019065	0.82[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2028216	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2071506	0.90[JPT][hapmap];0.80[EUR][1000 genomes]
rs2071507	0.95[JPT][hapmap]
rs2071508	0.90[JPT][hapmap];0.80[EUR][1000 genomes]
rs2072390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2079929	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2083180	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2109634	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2118540	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs2159644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2164884	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs2164885	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2230534	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2230535	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2239549	0.90[JPT][hapmap];0.87[EUR][1000 genomes]
rs2239550	0.86[EUR][1000 genomes]
rs2239551	0.90[JPT][hapmap];0.88[EUR][1000 genomes]
rs2239699	0.88[JPT][hapmap]
rs2240919	0.90[JPT][hapmap]
rs2240920	0.95[JPT][hapmap]
rs2268023	0.90[JPT][hapmap]
rs2268024	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2268025	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2268026	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2268027	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2270197	0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs2276824	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs2284350	0.82[EUR][1000 genomes]
rs2286798	0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs2286800	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2289247	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2289250	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2300149	0.90[JPT][hapmap];0.87[EUR][1000 genomes]
rs2336145	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2336146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs2336149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2336542	0.96[CEU][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2336545	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2535629	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2577831	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2590838	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2590846	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2710323	0.81[JPT][hapmap]
rs2878726	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs33967311	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34017441	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34157897	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34168767	0.81[EUR][1000 genomes]
rs34173654	0.80[ASN][1000 genomes]
rs34215106	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34291015	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34537256	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34610142	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34610878	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34739010	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34754793	0.86[EUR][1000 genomes]
rs34757451	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34918356	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34954168	0.81[EUR][1000 genomes]
rs35211965	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35212380	0.82[ASN][1000 genomes]
rs35249778	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35315313	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35409678	0.82[ASN][1000 genomes]
rs35526119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35976524	0.83[ASN][1000 genomes]
rs3617	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs3733039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3733041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3733045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3755798	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3755806	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3774354	0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs3774355	0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs3774365	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3774366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3852066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs4130905	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4435633	0.83[EUR][1000 genomes]
rs4687546	0.83[EUR][1000 genomes]
rs4687548	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4687549	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4687550	0.90[JPT][hapmap]
rs4687551	0.85[JPT][hapmap]
rs4687629	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs4687633	0.82[EUR][1000 genomes]
rs4687636	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4687637	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4687638	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4687639	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4687644	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4687648	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4687650	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62253700	0.82[EUR][1000 genomes]
rs62253703	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62253733	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62255362	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62255371	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62255396	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6414570	0.87[EUR][1000 genomes]
rs6445529	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6445531	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6445534	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6445535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6617	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67539070	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6762457	0.81[EUR][1000 genomes]
rs6762813	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6768697	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6770463	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6778329	0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs678	0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs6787154	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6792369	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs68021750	0.82[EUR][1000 genomes]
rs6803012	0.91[CEU][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6804145	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6805156	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs6976	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs736408	0.81[JPT][hapmap]
rs7611731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7614498	0.84[EUR][1000 genomes]
rs7620039	0.86[ASN][1000 genomes]
rs7622694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7624716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7625743	0.84[EUR][1000 genomes]
rs7628578	0.82[EUR][1000 genomes]
rs7638162	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7642198	0.81[EUR][1000 genomes]
rs7646741	0.89[ASN][1000 genomes]
rs7652191	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs7653028	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs767418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8906	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9324	0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs9879090	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs9881468	0.90[JPT][hapmap]
rs9917834	0.86[EUR][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	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
2	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
3	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1010761	chr3:52804547-52851258	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs998909	PBRM1	cis	Thyroid	GTEx
rs998909	NT5DC2	cis	multi-tissue	Pritchard
rs998909	NT5DC2	cis	Skin Sun Exposed Lower leg	GTEx
rs998909	FLJ12442	cis	multi-tissue	Pritchard
rs998909	PBRM1	cis	Artery Tibial	GTEx
rs998909	GLT8D1	Cis_1M	lymphoblastoid	RTeQTL
rs998909	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs998909	NT5DC2	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52803400-52805600	Active TSS	NHDF-Ad	bronchial
2	chr3:52803600-52805600	Active TSS	A549	lung
3	chr3:52803600-52806000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:52803800-52805200	Active TSS	NH-A	brain
5	chr3:52803800-52805400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:52803800-52805400	Active TSS	Fetal Intestine Large	intestine
7	chr3:52803800-52805400	Active TSS	Fetal Intestine Small	intestine
8	chr3:52803800-52805600	Active TSS	H1 Cell Line	embryonic stem cell
9	chr3:52803800-52805600	Active TSS	H9 Cell Line	embryonic stem cell
10	chr3:52803800-52805600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr3:52803800-52805600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:52803800-52805600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr3:52803800-52805600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:52803800-52805600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:52803800-52805800	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr3:52803800-52805800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:52803800-52805800	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr3:52804000-52805400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr3:52804000-52805400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr3:52804000-52805400	Active TSS	Muscle Satellite Cultured Cells	--
21	chr3:52804000-52805400	Active TSS	K562	blood
22	chr3:52804000-52805400	Active TSS	NHLF	lung
23	chr3:52804000-52805600	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr3:52804000-52805600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:52804000-52805600	Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr3:52804000-52805600	Active TSS	Aorta	Aorta
27	chr3:52804000-52805600	Active TSS	Gastric	stomach
28	chr3:52804000-52805800	Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr3:52804200-52805200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
30	chr3:52804200-52805200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr3:52804200-52805200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr3:52804200-52805200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr3:52804200-52805200	Active TSS	HMEC	breast
34	chr3:52804200-52805200	Active TSS	NHEK	skin
35	chr3:52804200-52805200	Active TSS	Osteobl	bone
36	chr3:52804200-52805400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr3:52804200-52805400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr3:52804200-52805400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:52804200-52805400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:52804200-52805400	Active TSS	Brain Anterior Caudate	brain
41	chr3:52804200-52805400	Active TSS	Brain Germinal Matrix	brain
42	chr3:52804200-52805400	Active TSS	Brain Hippocampus Middle	brain
43	chr3:52804200-52805400	Active TSS	Brain Inferior Temporal Lobe	brain
44	chr3:52804200-52805400	Active TSS	Esophagus	oesophagus
45	chr3:52804200-52805400	Active TSS	Fetal Brain Male	brain
46	chr3:52804200-52805400	Active TSS	Fetal Kidney	kidney
47	chr3:52804200-52805400	Active TSS	Fetal Lung	lung
48	chr3:52804200-52805400	Active TSS	Fetal Muscle Trunk	muscle
49	chr3:52804200-52805400	Active TSS	Fetal Stomach	stomach
50	chr3:52804200-52805400	Active TSS	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

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