Variant report

Variant	rs4680588
Chromosome Location	chr3:160192518-160192519
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr3:160191649-160192748	SK-N-SH	brain:	n/a	chr3:160192642-160192652
2	FOSL2	chr3:160191012-160192665	SK-N-SH	brain:	n/a	chr3:160191282-160191292 chr3:160191282-160191292 chr3:160191282-160191292 chr3:160191282-160191292 chr3:160191282-160191291
3	EP300	chr3:160191497-160192904	SK-N-SH	brain:	n/a	chr3:160191574-160191588
4	JUND	chr3:160191638-160192816	SK-N-SH	brain:	n/a	n/a
5	PBX3	chr3:160191649-160192784	SK-N-SH	brain:	n/a	n/a
6	GATA3	chr3:160191485-160192911	SK-N-SH	brain:	n/a	chr3:160191576-160191586
7	NFIC	chr3:160190976-160193068	SK-N-SH	brain:	n/a	chr3:160192549-160192577 chr3:160192454-160192471
8	TCF12	chr3:160190943-160192899	SK-N-SH	brain:	n/a	n/a
9	RXRA	chr3:160191653-160192718	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr3:160191660-160192899	SK-N-SH	brain:	n/a	n/a
11	RAD21	chr3:160192174-160192680	SK-N-SH_RA	brain:	n/a	n/a
12	MAX	chr3:160191596-160192637	SK-N-SH	brain:	n/a	n/a
13	EP300	chr3:160191709-160192691	SK-N-SH_RA	brain:	n/a	n/a
14	CTCF	chr3:160192420-160192570	NHEK	skin:	n/a	n/a
15	ZBTB33	chr3:160191669-160192565	SK-N-SH	brain:	n/a	n/a
16	GATA3	chr3:160191639-160192886	SK-N-SH	brain:	n/a	n/a
17	EP300	chr3:160191567-160192805	SK-N-SH	brain:	n/a	chr3:160191574-160191588
18	TEAD4	chr3:160191605-160192698	SK-N-SH	brain:	n/a	n/a
19	JUND	chr3:160191620-160193019	SK-N-SH	brain:	n/a	n/a
20	SIN3AK20	chr3:160191732-160192553	SK-N-SH	brain:	n/a	n/a
21	TEAD4	chr3:160191683-160192631	SK-N-SH	brain:	n/a	n/a
22	TCF12	chr3:160190823-160193016	SK-N-SH	brain:	n/a	n/a
23	PBX3	chr3:160191694-160192769	SK-N-SH	brain:	n/a	n/a
24	RAD21	chr3:160192227-160192540	SK-N-SH_RA	brain:	n/a	n/a
25	NFIC	chr3:160191651-160192841	SK-N-SH	brain:	n/a	chr3:160192549-160192577 chr3:160192454-160192471
26	EP300	chr3:160191729-160192705	SK-N-SH_RA	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:160191885..160194224-chr3:160197064..160198721,2	MCF-7	breast:
2	chr3:160166132..160171607-chr3:160191923..160195209,5	K562	blood:
3	chr3:160184913..160186500-chr3:160191059..160193425,2	K562	blood:

Variant related genes	Relation type
RNU7-136P	TF binding region
ENSG00000213186	Chromatin interaction
ENSG00000244009	Chromatin interaction

Extended variants
information (count: 112 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10212236	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1047210	0.85[CEU][hapmap]
rs10513551	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11706810	0.85[CEU][hapmap]
rs11918749	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1317365	0.81[CEU][hapmap];0.87[GIH][hapmap]
rs13403	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1451761	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1451762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1451764	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1551190	0.94[ASW][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.88[LWK][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1584688	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17236473	0.85[CEU][hapmap];0.84[JPT][hapmap]
rs17236544	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.86[ASN][1000 genomes]
rs17570467	0.96[CEU][hapmap];0.83[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap]
rs17826221	0.85[CEU][hapmap]
rs1882126	0.96[CEU][hapmap];0.83[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap]
rs1882127	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1920642	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1920662	0.86[ASN][1000 genomes]
rs1920664	0.83[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.84[TSI][hapmap];0.86[ASN][1000 genomes]
rs1953506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2152425	0.88[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2279457	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2305407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2366969	0.82[AMR][1000 genomes]
rs28705750	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2886825	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3773372	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3851365	0.85[CEU][hapmap]
rs3851366	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4091703	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41272947	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4621370	0.86[ASN][1000 genomes]
rs4679879	0.82[YRI][hapmap]
rs4679880	0.81[YRI][hapmap]
rs4679881	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4679885	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4679888	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4679889	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4679890	0.92[CEU][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4679891	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4679899	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4680576	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4680579	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4680580	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4680585	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4680587	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55687857	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs55731730	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56197102	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56394279	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58322641	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58665246	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs60009222	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60460891	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62272186	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62272791	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62272792	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62272794	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62272800	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6441313	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6441314	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6441319	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6441320	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6441324	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6768975	1.00[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6778728	0.82[YRI][hapmap]
rs6791261	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6792612	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6793560	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6798183	0.85[CEU][hapmap]
rs6798668	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6801300	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6803828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6808083	0.94[CHB][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6809153	0.85[CEU][hapmap]
rs6809313	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs721022	0.80[CEU][hapmap];0.83[GIH][hapmap]
rs721023	0.83[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73154592	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7356111	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7611130	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7618974	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7620828	0.84[CEU][hapmap]
rs7621724	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7624902	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.92[YRI][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7627555	0.85[CEU][hapmap]
rs7627749	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7627756	0.83[ASW][hapmap];0.92[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7629	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7629202	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7629423	0.80[JPT][hapmap]
rs7631792	0.83[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7634108	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7634826	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7640072	0.96[CEU][hapmap];0.83[CHB][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7643779	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7645832	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7647873	0.83[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs869468	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9798898	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9799314	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9862595	0.83[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.87[ASN][1000 genomes]
rs9968151	0.83[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	esv1800136	chr3:159950498-160278160	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	esv1801767	chr3:159950498-160279411	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
6	nsv1008519	chr3:160038710-160292589	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	255 gene(s)	inside rSNPs	diseases
7	esv1801686	chr3:160089896-160248363	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	211 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4680588	IFT80	cis	parietal	SCAN
rs4680588	EGFL6	trans	lymphoblastoid	seeQTL
rs4680588	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160189800-160193400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:160189800-160193400	Enhancers	HMEC	breast
3	chr3:160190200-160192800	Enhancers	HSMM	muscle
4	chr3:160190200-160193000	Enhancers	NHLF	lung
5	chr3:160190200-160193400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr3:160190200-160194200	Enhancers	Muscle Satellite Cultured Cells	--
7	chr3:160190400-160193000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr3:160190400-160193200	Enhancers	NHEK	skin
9	chr3:160190600-160199600	Weak transcription	Brain Substantia Nigra	brain
10	chr3:160191000-160193000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:160191200-160192600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:160192200-160192600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:160192200-160192600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr3:160192200-160192600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr3:160192200-160192600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:160192400-160193000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:160192400-160193400	Enhancers	NH-A	brain
18	chr3:160192400-160193600	Enhancers	NHDF-Ad	bronchial
19	chr3:160192400-160194400	Enhancers	Osteobl	bone
20	chr3:160192400-160195600	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links