Variant report

Variant	rs6568583
Chromosome Location	chr6:109911847-109911848
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 200 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:194)

rs_ID	r²[population]
rs10457201	0.84[EUR][1000 genomes]
rs10872041	0.82[EUR][1000 genomes]
rs10872047	0.82[EUR][1000 genomes]
rs10872051	0.82[EUR][1000 genomes]
rs10872052	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs1096136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1096138	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1096139	0.80[EUR][1000 genomes]
rs1096142	0.80[EUR][1000 genomes]
rs11153193	0.82[EUR][1000 genomes]
rs11153200	0.84[EUR][1000 genomes]
rs11153201	0.83[EUR][1000 genomes]
rs1115977	0.85[EUR][1000 genomes]
rs11751112	0.93[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap]
rs11753828	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs11754263	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11757485	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs11966009	0.81[EUR][1000 genomes]
rs11968485	0.81[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs12200787	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12204769	0.84[EUR][1000 genomes]
rs12211805	0.80[EUR][1000 genomes]
rs12215867	0.81[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs12524352	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs1321327	0.80[CEU][hapmap];0.84[EUR][1000 genomes]
rs1406957	0.81[CEU][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs1474959	0.81[CEU][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs1570011	0.83[EUR][1000 genomes]
rs1570012	0.84[EUR][1000 genomes]
rs1570013	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs1575109	0.84[EUR][1000 genomes]
rs17540056	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs17612758	0.81[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap]
rs17612996	0.82[YRI][hapmap]
rs1925921	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1967725	0.85[EUR][1000 genomes]
rs1969710	0.85[EUR][1000 genomes]
rs1969711	0.85[EUR][1000 genomes]
rs2016207	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs2064820	0.82[EUR][1000 genomes]
rs2064822	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2145144	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs2232448	0.95[MKK][hapmap];0.83[YRI][hapmap]
rs2357123	0.82[EUR][1000 genomes]
rs2357125	0.84[EUR][1000 genomes]
rs2357127	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2357128	0.83[TSI][hapmap]
rs2357130	0.82[EUR][1000 genomes]
rs2884101	0.82[EUR][1000 genomes]
rs4296926	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4454170	0.82[EUR][1000 genomes]
rs4523125	0.81[CEU][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs4591898	0.81[EUR][1000 genomes]
rs4946982	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4946986	0.82[EUR][1000 genomes]
rs4946987	0.82[EUR][1000 genomes]
rs4946989	0.84[EUR][1000 genomes]
rs4946991	0.84[EUR][1000 genomes]
rs4946992	0.81[CEU][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs4946995	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4946996	0.83[EUR][1000 genomes]
rs4946997	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4946998	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4946999	0.82[EUR][1000 genomes]
rs4947003	0.81[EUR][1000 genomes]
rs4947004	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4947006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56125306	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56264193	0.80[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61170920	0.82[EUR][1000 genomes]
rs62437563	0.86[EUR][1000 genomes]
rs6568578	1.00[CHB][hapmap]
rs6568579	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6568582	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6568586	0.81[EUR][1000 genomes]
rs6568590	0.81[EUR][1000 genomes]
rs6568591	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6568595	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs6568601	0.86[EUR][1000 genomes]
rs6568602	0.80[TSI][hapmap]
rs6568603	0.80[TSI][hapmap]
rs67715693	0.82[EUR][1000 genomes]
rs6900133	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6900187	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911851	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6912368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6916239	0.84[CEU][hapmap]
rs6917300	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6921303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6924269	0.81[CEU][hapmap]
rs6924436	0.88[EUR][1000 genomes]
rs6925886	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6929823	0.83[EUR][1000 genomes]
rs6931630	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6932774	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6938741	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6942171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.86[EUR][1000 genomes]
rs731879	0.81[EUR][1000 genomes]
rs7450970	0.81[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs7453835	0.80[CEU][hapmap];0.85[EUR][1000 genomes]
rs7454678	0.85[EUR][1000 genomes]
rs7744981	0.81[CEU][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs7745469	0.81[CEU][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs7749386	0.85[EUR][1000 genomes]
rs7749910	0.81[CEU][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs7754118	0.85[EUR][1000 genomes]
rs7754606	0.85[EUR][1000 genomes]
rs7756284	0.81[CEU][hapmap];0.82[YRI][hapmap]
rs7761008	0.80[CEU][hapmap];0.83[EUR][1000 genomes]
rs7764783	0.81[EUR][1000 genomes]
rs7765265	0.82[EUR][1000 genomes]
rs7769789	1.00[CHB][hapmap]
rs7771729	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7772109	0.87[EUR][1000 genomes]
rs7773915	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7775420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829815	0.81[EUR][1000 genomes]
rs829816	0.81[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs829817	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs911022	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs911023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320290	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320294	0.80[EUR][1000 genomes]
rs9320295	0.81[EUR][1000 genomes]
rs9320296	0.81[EUR][1000 genomes]
rs9320299	0.83[EUR][1000 genomes]
rs9320300	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320303	1.00[CEU][hapmap]
rs9320304	0.80[CEU][hapmap];0.85[EUR][1000 genomes]
rs9320305	0.85[EUR][1000 genomes]
rs9372216	0.83[EUR][1000 genomes]
rs9372220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9372221	0.80[CEU][hapmap];0.84[EUR][1000 genomes]
rs9372222	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs9374095	0.80[CEU][hapmap];0.82[EUR][1000 genomes]
rs9374096	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9374097	0.81[CEU][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs9374099	0.82[EUR][1000 genomes]
rs9374108	0.80[CEU][hapmap];0.85[EUR][1000 genomes]
rs9374113	0.81[EUR][1000 genomes]
rs9374114	0.81[EUR][1000 genomes]
rs9384713	0.82[EUR][1000 genomes]
rs9384715	0.83[EUR][1000 genomes]
rs9384716	0.84[EUR][1000 genomes]
rs9384717	0.83[TSI][hapmap]
rs9384720	0.81[EUR][1000 genomes]
rs9386812	0.82[EUR][1000 genomes]
rs9386813	0.81[CEU][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs9386814	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9386816	0.82[EUR][1000 genomes]
rs9386818	0.85[EUR][1000 genomes]
rs9386823	0.85[EUR][1000 genomes]
rs9386824	0.81[CEU][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs9386825	0.85[EUR][1000 genomes]
rs9386826	0.84[EUR][1000 genomes]
rs9398204	0.80[EUR][1000 genomes]
rs9398206	0.84[EUR][1000 genomes]
rs9400289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9400291	0.82[EUR][1000 genomes]
rs9400294	0.82[EUR][1000 genomes]
rs9400295	0.82[EUR][1000 genomes]
rs9400300	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9400301	0.85[EUR][1000 genomes]
rs9400307	0.82[EUR][1000 genomes]
rs9400310	0.81[CEU][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs9400312	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs9400313	0.81[EUR][1000 genomes]
rs9400315	0.81[EUR][1000 genomes]
rs9400316	0.81[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs9480973	0.80[CEU][hapmap];0.82[EUR][1000 genomes]
rs9480974	0.82[EUR][1000 genomes]
rs9480976	0.82[EUR][1000 genomes]
rs9480982	0.85[EUR][1000 genomes]
rs9480984	0.81[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs9480985	0.83[EUR][1000 genomes]
rs9480986	0.81[EUR][1000 genomes]
rs9480991	0.81[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs9487141	0.82[EUR][1000 genomes]
rs9487148	0.82[EUR][1000 genomes]
rs9487156	0.84[EUR][1000 genomes]
rs9487160	0.85[EUR][1000 genomes]
rs9487164	0.84[EUR][1000 genomes]
rs9487170	0.85[EUR][1000 genomes]
rs9487171	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs9487172	0.81[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs9487175	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs9487176	0.81[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs9487178	0.83[EUR][1000 genomes]
rs9487180	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs971432	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs971433	0.81[EUR][1000 genomes]
rs9968792	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9986423	0.81[EUR][1000 genomes]
rs9986507	0.81[CEU][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]

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	nsv1026012	chr6:109851638-109999379	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv604484	chr6:109851937-109997529	ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1019389	chr6:109868058-109987502	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv538416	chr6:109868058-109987502	Genic enhancers ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv917318	chr6:109885195-109982375	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv949475	chr6:109907936-110160501	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6568583	SMPD2	cis	Whole Blood	GTEx
rs6568583	AKD1	cis	lymphoblastoid	seeQTL
rs6568583	C6orf199	Cis_1M	lymphoblastoid	RTeQTL
rs6568583	FIG4	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109879000-109917400	Weak transcription	Aorta	Aorta
2	chr6:109911200-109912400	Enhancers	Primary T cells from cord blood	blood
3	chr6:109911800-109912400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr6:109911800-109912400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr6:109911800-109912400	Enhancers	Primary T helper cells PMA-I stimulated	--

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