Variant report

Variant	rs2797412
Chromosome Location	chr1:114302966-114302967
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:42)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:42 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CCNT2	chr1:114301360-114303041	K562	blood:	n/a	n/a
2	CTCF	chr1:114302651-114302993	K562	blood:	n/a	n/a
3	ZNF384	chr1:114300633-114303120	K562	blood:	n/a	n/a
4	KAP1	chr1:114301776-114303158	HEK293	kidney:	n/a	chr1:114302936-114302944
5	MAX	chr1:114300833-114303033	MCF-7	breast:	n/a	n/a
6	POLR2A	chr1:114301381-114302981	K562	blood:	n/a	n/a
7	MTA3	chr1:114301157-114303151	GM12878	blood:	n/a	n/a
8	GATA1	chr1:114301701-114303283	PBDE	blood:	n/a	n/a
9	CTCF	chr1:114302951-114303010	Hela-S3	cervix:	n/a	n/a
10	RELA	chr1:114301897-114303063	GM18951	blood:	n/a	n/a
11	TBL1XR1	chr1:114301743-114303216	K562	blood:	n/a	n/a
12	MXI1	chr1:114302257-114303005	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr1:114300923-114303939	GM12878	blood:	n/a	n/a
14	POLR2A	chr1:114301409-114302981	U87	brain:	n/a	n/a
15	ZC3H11A	chr1:114301331-114303033	K562	blood:	n/a	n/a
16	MYC	chr1:114300893-114303099	K562	blood:	n/a	n/a
17	POLR2A	chr1:114301407-114303227	K562	blood:	n/a	n/a
18	ZNF384	chr1:114300698-114303015	GM12878	blood:	n/a	n/a
19	ARID3A	chr1:114301853-114303029	K562	blood:	n/a	n/a
20	POLR2A	chr1:114301482-114303141	PANC-1	pancreas:	n/a	n/a
21	CTCF	chr1:114302898-114303019	Gliobla	brain:	n/a	n/a
22	MYC	chr1:114301390-114303048	NB4	blood:	n/a	n/a
23	MAX	chr1:114300755-114302981	NB4	blood:	n/a	n/a
24	POLR2A	chr1:114300640-114303489	GM12891	blood:	n/a	n/a
25	POLR2A	chr1:114301364-114303145	GM12878	blood:	n/a	n/a
26	RCOR1	chr1:114301295-114303204	K562	blood:	n/a	n/a
27	POLR2A	chr1:114301541-114303093	GM12878	blood:	n/a	n/a
28	NR2F2	chr1:114301479-114303170	K562	blood:	n/a	n/a
29	POLR2A	chr1:114301437-114302980	K562	blood:	n/a	n/a
30	WRNIP1	chr1:114301854-114303059	GM12878	blood:	n/a	n/a
31	POLR2A	chr1:114302965-114303370	HepG2	liver:	n/a	n/a
32	POLR2A	chr1:114301365-114303328	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr1:114301430-114303072	GM18951	blood:	n/a	n/a
34	CBX3	chr1:114301908-114303158	K562	blood:	n/a	n/a
35	POLR2A	chr1:114301460-114302998	MCF-7	breast:	n/a	n/a
36	TEAD4	chr1:114301624-114303149	K562	blood:	n/a	n/a
37	JUND	chr1:114301061-114303022	K562	blood:	n/a	chr1:114302092-114302103
38	POLR2A	chr1:114301331-114302995	K562	blood:	n/a	n/a
39	POLR2A	chr1:114301840-114303002	K562	blood:	n/a	n/a
40	POLR2A	chr1:114300917-114303400	K562	blood:	n/a	n/a
41	POLR2A	chr1:114301607-114303070	SK-N-SH	brain:	n/a	n/a
42	POLR2A	chr1:114300980-114305965	K562	blood:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:114301552..114304210-chr11:59521950..59524919,2	MCF-7	breast:
2	chr1:114300040..114303354-chr1:114351974..114356702,9	MCF-7	breast:
3	chr1:114300920..114303595-chr20:48598216..48600704,4	MCF-7	breast:
4	chr1:114301057..114304105-chr1:114310097..114314111,4	MCF-7	breast:
5	chr1:114298167..114305255-chr1:114351008..114356451,27	MCF-7	breast:
6	chr1:114302807..114305155-chr1:114318148..114320872,2	K562	blood:
7	chr1:114300422..114303875-chr1:114445198..114448512,7	MCF-7	breast:
8	chr1:114302426..114304248-chr1:114378191..114380113,2	MCF-7	breast:
9	chr1:114301163..114303418-chr1:114471834..114473459,2	K562	blood:
10	chr1:114299507..114303267-chr1:114354438..114356409,4	K562	blood:
11	chr1:114300956..114303148-chr11:59521456..59522999,2	MCF-7	breast:
12	chr1:114300189..114305139-chr20:48598182..48603040,8	MCF-7	breast:
13	chr1:114302137..114303068-chr3:73159954..73160572,2	Hela-S3	cervix:
14	chr1:114247347..114249870-chr1:114302601..114305068,2	MCF-7	breast:

No data

Variant related genes	Relation type
PHTF1	TF binding region
ENSG00000163349	Chromatin interaction
ENSG00000166900	Chromatin interaction
ENSG00000254477	Chromatin interaction
ENSG00000124216	Chromatin interaction
ENSG00000231128	Chromatin interaction
ENSG00000223247	Chromatin interaction
ENSG00000118655	Chromatin interaction
ENSG00000235527	Chromatin interaction
ENSG00000116793	Chromatin interaction
ENSG00000134262	Chromatin interaction
ENSG00000081019	Chromatin interaction

Extended variants
information (count: 142 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:140)

rs_ID	r²[population]
rs10858005	0.82[CEU][hapmap];0.81[CHB][hapmap];0.80[EUR][1000 genomes]
rs10858007	0.82[CEU][hapmap];0.81[CHB][hapmap];0.94[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs10858008	0.82[CEU][hapmap];0.81[CHB][hapmap];0.97[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs10858011	0.82[CEU][hapmap];0.81[CHB][hapmap];0.97[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs10858017	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10858018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10858019	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10858021	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11102653	0.80[EUR][1000 genomes]
rs11102654	0.81[CHB][hapmap];0.80[EUR][1000 genomes]
rs11102661	0.85[EUR][1000 genomes]
rs11102669	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11102689	0.80[EUR][1000 genomes]
rs11102691	0.95[CEU][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs1111695	0.81[YRI][hapmap]
rs1113523	0.82[CEU][hapmap];0.86[CHB][hapmap];0.97[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs1146182	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1146187	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12041547	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12044534	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12061482	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];1.00[TSI][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12063216	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12077419	0.80[EUR][1000 genomes]
rs1217192	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[GIH][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs1217193	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[EUR][1000 genomes]
rs1217199	0.81[CEU][hapmap];0.81[CHB][hapmap];0.81[EUR][1000 genomes]
rs1217200	0.90[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.85[EUR][1000 genomes]
rs1217201	0.82[CEU][hapmap];0.81[CHB][hapmap];0.97[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs1217203	0.81[EUR][1000 genomes]
rs1217204	0.81[EUR][1000 genomes]
rs1217210	0.91[EUR][1000 genomes]
rs1217211	0.82[CEU][hapmap];0.86[CHB][hapmap];0.81[EUR][1000 genomes]
rs1217214	0.80[EUR][1000 genomes]
rs1217215	0.80[EUR][1000 genomes]
rs1217223	0.81[EUR][1000 genomes]
rs1217226	0.82[CEU][hapmap];0.81[CHB][hapmap];0.97[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes]
rs1217227	0.82[CEU][hapmap];0.81[CHB][hapmap];0.97[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs1217228	0.82[CEU][hapmap];0.81[CHB][hapmap];0.97[GIH][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs1217230	0.81[EUR][1000 genomes]
rs1217232	0.81[EUR][1000 genomes]
rs1217233	0.81[EUR][1000 genomes]
rs1217234	0.82[CEU][hapmap];0.81[CHB][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs1217235	0.82[CEU][hapmap];0.81[CHB][hapmap];0.90[YRI][hapmap];0.81[EUR][1000 genomes]
rs1217236	0.82[CEU][hapmap];0.94[GIH][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs1217237	0.81[EUR][1000 genomes]
rs1217376	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1217377	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1217380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1217386	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1217388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1217389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1217395	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1217396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1217407	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1217410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1217412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1217413	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1217415	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap]
rs1217416	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1217421	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1230637	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1230638	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1230639	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1230640	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];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1230642	0.85[ASN][1000 genomes]
rs1230645	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1230646	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1230647	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];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1230649	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1230655	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1230656	0.82[EUR][1000 genomes]
rs1230658	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1230659	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1230661	0.82[CEU][hapmap];0.86[CHB][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs1230663	0.87[EUR][1000 genomes]
rs1230671	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1230674	0.85[EUR][1000 genomes]
rs1230678	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1230679	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1230680	0.97[AFR][1000 genomes]
rs1230682	0.83[AFR][1000 genomes]
rs1230683	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1230685	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1230686	0.83[AFR][1000 genomes]
rs1230687	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1235687	0.81[EUR][1000 genomes]
rs1235688	0.81[EUR][1000 genomes]
rs1237289	0.82[CEU][hapmap];0.81[CHB][hapmap];0.81[EUR][1000 genomes]
rs1237682	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12565589	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs12566340	0.95[CEU][hapmap];0.81[CHB][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs12760067	0.81[ASN][1000 genomes]
rs1343125	0.82[CEU][hapmap];0.97[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs1343128	0.85[CEU][hapmap];0.81[CHB][hapmap];0.97[GIH][hapmap];0.94[TSI][hapmap];0.80[EUR][1000 genomes]
rs1418958	0.82[CEU][hapmap];0.81[CHB][hapmap];0.81[EUR][1000 genomes]
rs1599971	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17031716	0.86[CHB][hapmap]
rs1743605	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1746853	0.81[CHB][hapmap]
rs1775754	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1777234	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1777237	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1777238	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1777241	0.89[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1935838	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1936398	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1981319	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];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2093436	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2243471	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2295853	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];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2359167	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2488457	0.90[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2488458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2636002	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2636013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2636014	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2797408	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2797409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2797414	0.90[ASW][hapmap];0.90[LWK][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes]
rs2798135	0.90[EUR][1000 genomes]
rs2798138	0.90[EUR][1000 genomes]
rs4145859	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4423005	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4565712	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4600045	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4838997	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4838998	0.86[ASN][1000 genomes]
rs4839335	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61817589	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6537792	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6537795	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6663679	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6698586	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];1.00[TSI][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6704188	0.81[CHB][hapmap];0.83[MEX][hapmap]
rs72687980	0.80[EUR][1000 genomes]
rs7526209	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7529353	0.95[CEU][hapmap];0.81[CHB][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs7536360	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs7553188	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9429730	1.00[CEU][hapmap];0.92[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	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv831093	chr1:114254167-114378235	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2797412	BCL2L15	cis	cerebellum	SCAN
rs2797412	CAPZA1	cis	parietal	SCAN
rs2797412	MAGI3	cis	cerebellum	SCAN
rs2797412	MAGI3	cis	parietal	SCAN
rs2797412	PHTF1	cis	parietal	SCAN
rs2797412	PHTF1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114300000-114303000	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr1:114300200-114303000	Active TSS	H1 Cell Line	embryonic stem cell
3	chr1:114300200-114303000	Active TSS	H9 Cell Line	embryonic stem cell
4	chr1:114300400-114303000	Active TSS	Fetal Intestine Large	intestine
5	chr1:114300400-114303000	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr1:114300400-114303400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:114300600-114303000	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr1:114300600-114303000	Active TSS	Colonic Mucosa	Colon
9	chr1:114300600-114303200	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr1:114301000-114303000	Active TSS	Fetal Brain Male	brain
11	chr1:114302200-114303000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
12	chr1:114302200-114303000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
13	chr1:114302200-114303000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
14	chr1:114302200-114303000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:114302200-114303000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr1:114302200-114303000	Flanking Active TSS	Dnd41	blood
17	chr1:114302200-114303000	Flanking Active TSS	Hela-S3	cervix
18	chr1:114302200-114303000	Flanking Active TSS	NH-A	brain
19	chr1:114302200-114303000	Flanking Active TSS	Osteobl	bone
20	chr1:114302200-114303800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:114302200-114304000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr1:114302400-114303000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:114302400-114303000	Flanking Active TSS	Primary hematopoietic stem cells	blood
24	chr1:114302400-114303000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
25	chr1:114302400-114303000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:114302400-114303000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr1:114302400-114303000	Flanking Active TSS	Adipose Nuclei	Adipose
28	chr1:114302400-114303000	Flanking Active TSS	Brain Germinal Matrix	brain
29	chr1:114302400-114303000	Flanking Active TSS	Fetal Brain Female	brain
30	chr1:114302400-114303000	Flanking Active TSS	Fetal Muscle Leg	muscle
31	chr1:114302400-114303000	Flanking Active TSS	NHLF	lung
32	chr1:114302400-114303200	Flanking Active TSS	GM12878-XiMat	blood
33	chr1:114302400-114303200	Flanking Active TSS	K562	blood
34	chr1:114302400-114303200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr1:114302400-114303400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr1:114302400-114303400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
37	chr1:114302400-114311800	Weak transcription	Small Intestine	intestine
38	chr1:114302600-114303000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr1:114302600-114303000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr1:114302600-114303000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
41	chr1:114302600-114303000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:114302600-114303000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr1:114302600-114303000	Flanking Active TSS	Primary B cells from cord blood	blood
44	chr1:114302600-114303000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr1:114302600-114303000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr1:114302600-114303000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr1:114302600-114303000	Flanking Active TSS	Brain Angular Gyrus	brain
48	chr1:114302600-114303000	Flanking Active TSS	Fetal Heart	heart
49	chr1:114302600-114303000	Flanking Active TSS	Fetal Kidney	kidney
50	chr1:114302600-114303000	Flanking Active TSS	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links