Variant report

Variant	rs6601333
Chromosome Location	chr8:9427048-9427049
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 116 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10087012	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10087166	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10087749	0.80[EUR][1000 genomes]
rs10088037	0.80[EUR][1000 genomes]
rs10088401	0.80[EUR][1000 genomes]
rs10088969	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10097438	0.81[EUR][1000 genomes]
rs10098758	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10101953	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10102030	0.94[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10103426	0.94[CEU][hapmap];0.86[CHB][hapmap];0.92[EUR][1000 genomes]
rs10103752	0.80[EUR][1000 genomes]
rs10111980	0.84[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10112600	0.81[EUR][1000 genomes]
rs10112821	0.80[EUR][1000 genomes]
rs10503380	0.82[CHD][hapmap];0.87[GIH][hapmap];0.84[EUR][1000 genomes]
rs10794712	0.83[CEU][hapmap]
rs10903314	0.94[GIH][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap]
rs11249931	0.83[JPT][hapmap]
rs11249938	0.94[CEU][hapmap]
rs11249942	0.83[CEU][hapmap]
rs11779335	0.83[CEU][hapmap];0.92[GIH][hapmap]
rs11984585	0.89[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11985349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11993506	0.89[JPT][hapmap];0.80[EUR][1000 genomes]
rs11994420	0.89[JPT][hapmap];0.80[EUR][1000 genomes]
rs11995920	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12541409	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12541617	0.81[CEU][hapmap]
rs12543534	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12545912	0.82[CEU][hapmap];0.94[GIH][hapmap]
rs12548306	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12674762	0.94[GIH][hapmap];0.93[MEX][hapmap]
rs12675476	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12675511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12676898	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12679892	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs12681719	0.94[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]
rs13249683	0.80[CEU][hapmap]
rs13271097	0.85[EUR][1000 genomes]
rs13273033	0.84[ASW][hapmap];0.83[CEU][hapmap];0.94[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap]
rs17150237	0.81[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28622033	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28668310	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28695930	0.80[EUR][1000 genomes]
rs33945943	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34206126	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34324628	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34790717	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4128199	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4240626	0.94[GIH][hapmap];0.83[JPT][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap]
rs4240629	0.83[CEU][hapmap]
rs4282575	0.80[EUR][1000 genomes]
rs4372006	0.81[EUR][1000 genomes]
rs4398920	0.94[GIH][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap]
rs4407883	0.89[JPT][hapmap];0.80[EUR][1000 genomes]
rs4493905	0.80[EUR][1000 genomes]
rs4535744	0.83[CEU][hapmap]
rs4568626	0.80[EUR][1000 genomes]
rs4582568	0.80[EUR][1000 genomes]
rs4626603	0.82[CEU][hapmap]
rs4840427	0.87[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.82[LWK][hapmap];0.88[ASN][1000 genomes]
rs4840428	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4841173	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4841174	0.94[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4841175	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4841179	0.97[GIH][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs4841212	0.83[CEU][hapmap];0.94[GIH][hapmap]
rs55917145	0.80[EUR][1000 genomes]
rs57453266	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58238328	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61551896	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62493868	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6601330	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6601331	0.94[CEU][hapmap];0.86[CHB][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6601332	0.94[CEU][hapmap];0.82[CHB][hapmap];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6601334	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6601335	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6601336	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6601337	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6601339	0.81[EUR][1000 genomes]
rs6651495	0.80[EUR][1000 genomes]
rs6651496	0.80[EUR][1000 genomes]
rs6651502	0.80[EUR][1000 genomes]
rs66516712	0.88[EUR][1000 genomes]
rs67706102	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6980831	0.94[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6985140	0.81[GIH][hapmap]
rs6986386	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6989126	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6990097	0.91[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6990590	0.94[CEU][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7010270	0.83[CEU][hapmap]
rs7013500	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73193784	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7461376	0.83[CEU][hapmap]
rs7462102	0.80[EUR][1000 genomes]
rs7462910	0.83[CEU][hapmap];0.92[GIH][hapmap]
rs7464185	0.80[EUR][1000 genomes]
rs7814014	0.94[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7815817	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7821559	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7822548	0.94[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7822904	0.82[CEU][hapmap]
rs7832096	0.83[CEU][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs7834823	0.94[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7841069	0.83[AMR][1000 genomes]
rs7841074	0.83[AMR][1000 genomes]
rs7844450	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7846140	0.94[CEU][hapmap];0.81[CHB][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9329202	0.86[CHB][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9329203	0.84[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9644677	0.86[CHD][hapmap];0.85[GIH][hapmap];0.94[MEX][hapmap];0.81[ASN][1000 genomes]
rs9650638	0.83[CEU][hapmap];0.82[CHB][hapmap]

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	nsv530864	chr8:9097498-9914548	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv497927	chr8:9097611-9544519	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6601333	FLJ10661	cis	cerebellum	SCAN
rs6601333	TNKS	cis	parietal	SCAN
rs6601333	TNKS	cis	cerebellum	SCAN
rs6601333	DEFB134	cis	cerebellum	SCAN
rs6601333	PRSS55	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:9414400-9459600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr8:9414800-9427800	Weak transcription	Right Ventricle	heart
3	chr8:9415000-9435400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr8:9415800-9434800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr8:9416000-9432400	Weak transcription	Primary B cells from cord blood	blood
6	chr8:9416000-9434600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr8:9416200-9432600	Weak transcription	Fetal Intestine Small	intestine
8	chr8:9416200-9434200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr8:9416600-9430200	Weak transcription	Brain Substantia Nigra	brain
10	chr8:9417000-9434600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr8:9417200-9427800	Weak transcription	Psoas Muscle	Psoas
12	chr8:9417200-9430000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr8:9417200-9434400	Weak transcription	Primary T cells from cord blood	blood
14	chr8:9417200-9450000	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr8:9417600-9427800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr8:9417600-9437600	Weak transcription	Dnd41	blood
17	chr8:9418000-9435000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr8:9418600-9434800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr8:9419400-9427800	Weak transcription	Ovary	ovary
20	chr8:9419600-9428200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr8:9420400-9429400	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr8:9421600-9427800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr8:9421600-9429400	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr8:9421800-9427800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr8:9422000-9432400	Weak transcription	Primary B cells from peripheral blood	blood
26	chr8:9422200-9438400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr8:9422400-9428200	Weak transcription	Brain Angular Gyrus	brain
28	chr8:9422400-9434600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr8:9424800-9440000	Weak transcription	Fetal Lung	lung
30	chr8:9425800-9429400	Weak transcription	Brain Anterior Caudate	brain
31	chr8:9425800-9435000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr8:9426200-9430800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr8:9426200-9431400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr8:9426400-9429400	Weak transcription	Brain Hippocampus Middle	brain
35	chr8:9426600-9427600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr8:9426600-9429600	Weak transcription	Brain Cingulate Gyrus	brain
37	chr8:9426800-9427400	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr8:9426800-9429400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr8:9427000-9430200	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr8:9427000-9435000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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