Variant report

Variant	rs17111594
Chromosome Location	chr10:98056598-98056599
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];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10786277	1.00[CHB][hapmap]
rs10786279	1.00[CHB][hapmap]
rs10882772	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.87[ASN][1000 genomes]
rs10882773	1.00[CHB][hapmap]
rs11188697	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11188702	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11188704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11188705	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11188709	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11591467	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.87[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];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12258764	0.84[CEU][hapmap];0.87[TSI][hapmap]
rs12269557	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];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12761473	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12761715	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];0.98[ASN][1000 genomes]
rs12763059	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12766367	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];0.98[ASN][1000 genomes]
rs12772674	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];0.98[ASN][1000 genomes]
rs12774154	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];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12779164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12779203	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12779564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17111598	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17111599	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17111603	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17111609	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];0.94[ASN][1000 genomes]
rs17111612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17111614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17111622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17111628	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17111733	1.00[CHB][hapmap]
rs1815258	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1923707	1.00[CHB][hapmap]
rs1923708	1.00[CHB][hapmap]
rs2146390	0.91[CEU][hapmap]
rs2146394	1.00[CHB][hapmap]
rs2181322	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2273891	1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap]
rs2861307	0.86[JPT][hapmap]
rs2861572	1.00[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap]
rs34125453	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34128907	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34220987	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34521234	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34943354	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35055142	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35259489	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35388328	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35531390	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35925896	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35933547	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36003947	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3789937	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];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3789938	0.84[CEU][hapmap];0.83[TSI][hapmap]
rs3818313	1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap]
rs4550161	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4917732	1.00[CHB][hapmap]
rs60349635	0.87[AFR][1000 genomes]
rs7073871	0.92[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[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7077344	0.83[GIH][hapmap];1.00[MEX][hapmap]
rs71482401	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71482402	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71484204	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71484205	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7893551	1.00[CHB][hapmap]
rs7917592	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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
rs17111594	GOT1	cis	cerebellum	SCAN
rs17111594	CHUK	cis	parietal	SCAN
rs17111594	OPALIN	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98048600-98058800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr10:98050600-98059200	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr10:98052800-98058400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr10:98053200-98059200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr10:98055200-98061000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr10:98055600-98056600	Flanking Active TSS	Fetal Thymus	thymus
7	chr10:98055800-98057000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr10:98055800-98058600	Weak transcription	Primary B cells from peripheral blood	blood
9	chr10:98055800-98058600	Weak transcription	Primary T cells from cord blood	blood
10	chr10:98055800-98058800	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr10:98055800-98059200	Weak transcription	GM12878-XiMat	blood
12	chr10:98056000-98057200	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr10:98056200-98056600	Weak transcription	Brain Germinal Matrix	brain
14	chr10:98056200-98057200	Enhancers	Dnd41	blood
15	chr10:98056200-98057400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr10:98056200-98057400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr10:98056200-98058800	Weak transcription	Primary B cells from cord blood	blood
18	chr10:98056400-98056600	Flanking Active TSS	Thymus	Thymus
19	chr10:98056400-98056800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr10:98056400-98056800	Weak transcription	Primary T helper cells PMA-I stimulated	--

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