Variant report

Variant	rs17111609
Chromosome Location	chr10:98059160-98059161
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10509708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10786277	1.00[CHB][hapmap]
rs10786279	1.00[CHB][hapmap]
rs10882772	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[ASN][1000 genomes]
rs10882773	1.00[CHB][hapmap]
rs11188697	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11188702	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11188704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11188705	0.90[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11188709	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11591467	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[ASN][1000 genomes]
rs11593073	1.00[CHB][hapmap]
rs11593074	1.00[CHB][hapmap]
rs11593503	1.00[CHB][hapmap]
rs11597348	0.85[CHB][hapmap]
rs11598258	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];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12258764	0.84[CEU][hapmap]
rs12269557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12761473	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12761715	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];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12763059	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12766367	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];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12772674	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];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12774154	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];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12779164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12779203	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12779564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17111594	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17111598	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17111599	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17111603	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17111612	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[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17111614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17111622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17111628	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17111733	1.00[CHB][hapmap]
rs1815258	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1923707	1.00[CHB][hapmap]
rs1923708	1.00[CHB][hapmap]
rs2146390	0.91[CEU][hapmap];0.81[TSI][hapmap]
rs2146394	1.00[CHB][hapmap]
rs2181322	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2273891	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes]
rs2861307	0.86[JPT][hapmap]
rs2861572	1.00[CHB][hapmap];0.81[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap]
rs34125453	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34128907	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34220987	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34521234	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34943354	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35055142	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35259489	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35388328	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35531390	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35925896	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35933547	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36003947	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3789937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3789938	0.84[CEU][hapmap]
rs3818313	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes]
rs4550161	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4917732	1.00[CHB][hapmap]
rs7073871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7077344	1.00[MEX][hapmap]
rs71482401	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71482402	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71484204	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71484205	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72811058	0.82[AMR][1000 genomes]
rs7893551	1.00[CHB][hapmap]
rs7917592	0.96[EUR][1000 genomes];0.96[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	esv3413353	chr10:98039370-98561524	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	esv2761620	chr10:98047045-98089749	Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17111609	CHUK	cis	parietal	SCAN
rs17111609	GOT1	cis	cerebellum	SCAN
rs17111609	OPALIN	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98050600-98059200	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr10:98053200-98059200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr10:98055200-98061000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr10:98055800-98059200	Weak transcription	GM12878-XiMat	blood
5	chr10:98056800-98062800	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr10:98057000-98059600	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr10:98057200-98061800	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr10:98057400-98060000	Flanking Active TSS	Thymus	Thymus
9	chr10:98057400-98061200	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr10:98057400-98062000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr10:98057600-98063800	Enhancers	Fetal Thymus	thymus
12	chr10:98057800-98060200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr10:98058000-98061400	Enhancers	Primary T cells fromperipheralblood	blood
14	chr10:98058400-98060000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr10:98058600-98059200	Enhancers	Primary B cells from peripheral blood	blood
16	chr10:98058600-98059200	Enhancers	Primary T cells from cord blood	blood
17	chr10:98058600-98060000	Enhancers	Brain Germinal Matrix	brain
18	chr10:98058800-98059200	Enhancers	Monocytes-CD14+_RO01746	blood
19	chr10:98058800-98060000	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
20	chr10:98058800-98060600	Enhancers	Primary hematopoietic stem cells	blood
21	chr10:98058800-98062800	Flanking Active TSS	Dnd41	blood
22	chr10:98059000-98059200	Flanking Active TSS	Primary B cells from cord blood	blood
23	chr10:98059000-98059400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
24	chr10:98059000-98059400	Enhancers	Colon Smooth Muscle	Colon

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