Variant report

Variant	rs6925886
Chromosome Location	chr6:109878515-109878516
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 167 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:163)

rs_ID	r²[population]
rs10457201	0.82[EUR][1000 genomes]
rs10872041	0.84[EUR][1000 genomes]
rs10872047	0.82[EUR][1000 genomes]
rs10872052	0.81[CEU][hapmap]
rs1096136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1096138	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11153193	0.80[EUR][1000 genomes]
rs1115977	0.81[EUR][1000 genomes]
rs11753828	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs11754263	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11966009	0.84[EUR][1000 genomes]
rs11968485	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs12200787	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12215867	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs12524352	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs1321327	0.80[CEU][hapmap]
rs1358759	0.81[EUR][1000 genomes]
rs1406957	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs1474959	0.81[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs1570011	0.83[EUR][1000 genomes]
rs1570012	0.82[EUR][1000 genomes]
rs1570013	0.81[CEU][hapmap]
rs1590187	0.81[EUR][1000 genomes]
rs17540056	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs17612758	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs1925921	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1967725	0.81[EUR][1000 genomes]
rs1969710	0.80[EUR][1000 genomes]
rs1969711	0.81[EUR][1000 genomes]
rs1985123	0.81[EUR][1000 genomes]
rs1998812	0.82[EUR][1000 genomes]
rs2016207	0.81[CEU][hapmap]
rs2064820	0.84[EUR][1000 genomes]
rs2064822	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2145144	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs2357123	0.84[EUR][1000 genomes]
rs2357125	0.82[EUR][1000 genomes]
rs2357127	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2357128	0.83[TSI][hapmap]
rs4296926	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4523125	0.81[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs4946982	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4946986	0.84[EUR][1000 genomes]
rs4946987	0.84[EUR][1000 genomes]
rs4946989	0.82[EUR][1000 genomes]
rs4946992	0.81[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs4946995	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4946997	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4946998	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4947004	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4947006	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56125306	0.86[EUR][1000 genomes]
rs56264193	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62437563	0.83[EUR][1000 genomes]
rs6568578	1.00[CHB][hapmap]
rs6568579	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6568580	0.81[EUR][1000 genomes]
rs6568582	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6568583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6568591	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6568595	0.81[CEU][hapmap]
rs6568601	0.83[EUR][1000 genomes]
rs6568602	0.80[TSI][hapmap]
rs6568603	0.80[TSI][hapmap]
rs67715693	0.82[EUR][1000 genomes]
rs6900133	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6900187	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911851	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6912368	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6916239	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs6917300	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6921303	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6924269	0.81[CEU][hapmap]
rs6924436	0.83[EUR][1000 genomes]
rs6929823	0.83[EUR][1000 genomes]
rs6931630	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6932774	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6938499	0.80[EUR][1000 genomes]
rs6938741	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6942171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs7450970	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs7453835	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs7454678	0.80[EUR][1000 genomes]
rs7744981	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs7745469	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs7749386	0.81[EUR][1000 genomes]
rs7749910	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs7754118	0.81[EUR][1000 genomes]
rs7754606	0.81[EUR][1000 genomes]
rs7761008	0.80[CEU][hapmap]
rs7769789	1.00[CHB][hapmap]
rs7771729	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7772109	0.83[EUR][1000 genomes]
rs7773915	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7775420	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829816	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs829817	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs911022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs911023	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320290	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320294	0.83[EUR][1000 genomes]
rs9320295	0.83[EUR][1000 genomes]
rs9320296	0.83[EUR][1000 genomes]
rs9320299	0.83[EUR][1000 genomes]
rs9320300	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320303	1.00[CEU][hapmap]
rs9320304	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs9320305	0.81[EUR][1000 genomes]
rs9372216	0.81[EUR][1000 genomes]
rs9372220	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9372221	0.80[CEU][hapmap]
rs9372222	0.81[CEU][hapmap]
rs9374092	0.80[EUR][1000 genomes]
rs9374095	0.80[CEU][hapmap];0.84[EUR][1000 genomes]
rs9374096	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9374097	0.81[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs9374098	0.81[EUR][1000 genomes]
rs9374099	0.84[EUR][1000 genomes]
rs9374108	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs9384713	0.84[EUR][1000 genomes]
rs9384715	0.83[EUR][1000 genomes]
rs9384716	0.82[EUR][1000 genomes]
rs9384717	0.83[TSI][hapmap]
rs9386812	0.84[EUR][1000 genomes]
rs9386813	0.81[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs9386814	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9386816	0.81[EUR][1000 genomes]
rs9386818	0.81[EUR][1000 genomes]
rs9386823	0.81[EUR][1000 genomes]
rs9386824	0.81[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs9386825	0.81[EUR][1000 genomes]
rs9398204	0.83[EUR][1000 genomes]
rs9398206	0.82[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];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9400291	0.84[EUR][1000 genomes]
rs9400294	0.84[EUR][1000 genomes]
rs9400295	0.84[EUR][1000 genomes]
rs9400300	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9400301	0.81[EUR][1000 genomes]
rs9400310	0.81[CEU][hapmap];0.84[TSI][hapmap]
rs9400312	0.81[CEU][hapmap]
rs9400316	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs942923	0.81[EUR][1000 genomes]
rs942924	0.82[EUR][1000 genomes]
rs9480973	0.80[CEU][hapmap];0.84[EUR][1000 genomes]
rs9480974	0.84[EUR][1000 genomes]
rs9480976	0.84[EUR][1000 genomes]
rs9480982	0.81[EUR][1000 genomes]
rs9480984	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs9480991	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs9487141	0.84[EUR][1000 genomes]
rs9487148	0.84[EUR][1000 genomes]
rs9487156	0.82[EUR][1000 genomes]
rs9487160	0.81[EUR][1000 genomes]
rs9487170	0.81[EUR][1000 genomes]
rs9487171	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs9487172	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs9487175	0.81[CEU][hapmap]
rs9487176	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs9487180	0.81[CEU][hapmap]
rs971432	0.81[CEU][hapmap]
rs9968792	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9986507	0.81[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6925886	FLJ42177	cis	multi-tissue	Pritchard
rs6925886	FIG4	cis	cerebellum	SCAN
rs6925886	SMPD2	cis	Whole Blood	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109867000-109885800	Weak transcription	Ovary	ovary
2	chr6:109870600-109878800	Weak transcription	Primary T cells from cord blood	blood
3	chr6:109871400-109884000	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr6:109878400-109878800	ZNF genes & repeats	Pancreas	Pancrea
5	chr6:109878400-109879000	ZNF genes & repeats	Left Ventricle	heart
6	chr6:109878400-109879000	ZNF genes & repeats	Thymus	Thymus
7	chr6:109878400-109879600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr6:109878400-109886200	Weak transcription	Rectal Mucosa Donor 31	rectum

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