Variant report

Variant	rs9636245
Chromosome Location	chr2:234970412-234970413
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10168712	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs10171064	1.00[ASN][1000 genomes]
rs10171587	0.89[CEU][hapmap];0.91[GIH][hapmap];0.80[MEX][hapmap];0.86[EUR][1000 genomes]
rs10172000	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs10178472	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10192448	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10193392	0.84[GIH][hapmap];0.81[TSI][hapmap]
rs10195232	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10197450	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10200368	1.00[CEU][hapmap];0.86[GIH][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs10205160	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs10210816	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10803669	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13389896	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13395783	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1354895	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs17864802	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17864805	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17869100	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1911592	0.89[CEU][hapmap];0.91[GIH][hapmap];0.80[MEX][hapmap];0.86[EUR][1000 genomes]
rs1911593	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs1911594	0.89[CEU][hapmap];0.91[GIH][hapmap];0.86[EUR][1000 genomes]
rs1911595	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2239536	1.00[ASN][1000 genomes]
rs2267900	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs2267901	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2267902	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs2267903	0.84[GIH][hapmap]
rs2267904	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs28903704	0.88[EUR][1000 genomes]
rs3771331	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs3819748	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4233639	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs4664004	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4664007	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs596463	0.83[GIH][hapmap]
rs620654	0.83[GIH][hapmap]
rs634613	0.87[GIH][hapmap];0.90[MEX][hapmap];0.89[AMR][1000 genomes]
rs665535	0.89[AMR][1000 genomes]
rs6739495	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs7603271	0.84[GIH][hapmap]
rs7608191	0.89[CEU][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv834571	chr2:234929288-235110332	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9636245	COL6A3	cis	parietal	SCAN
rs9636245	GPR55	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234965600-234971200	Genic enhancers	Liver	Liver
2	chr2:234966200-234970800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:234969200-234970800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:234970400-234970800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr2:234970400-234971200	Enhancers	Primary T cells fromperipheralblood	blood
6	chr2:234970400-234971200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr2:234970400-234971200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr2:234970400-234971200	Enhancers	Primary T killer memory cells from peripheral blood	blood

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