Variant report

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10212191	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs10510736	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs17391070	0.92[YRI][hapmap]
rs2001682	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs28435122	0.86[EUR][1000 genomes]
rs28548208	0.86[EUR][1000 genomes]
rs2948619	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs531888	0.89[CEU][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs532792	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs55701670	0.81[EUR][1000 genomes]
rs62247060	0.85[EUR][1000 genomes]
rs62247061	0.85[EUR][1000 genomes]
rs62247062	0.85[EUR][1000 genomes]
rs62247128	0.81[AFR][1000 genomes]
rs6442134	0.83[EUR][1000 genomes]
rs644534	0.96[CEU][hapmap];0.85[TSI][hapmap];0.91[EUR][1000 genomes]
rs6764648	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs6794402	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs6806427	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs704903	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7633590	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs7643433	0.85[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs834177	0.89[CEU][hapmap]
rs872126	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs9311332	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs9812262	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs9848904	0.96[CEU][hapmap];0.85[TSI][hapmap];0.91[EUR][1000 genomes]
rs9858123	0.81[EUR][1000 genomes]
rs9874514	0.83[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	nsv460522	chr3:42967597-43175207	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv590149	chr3:42967597-43175207	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv432417	chr3:43045796-43098296	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13087788	CCR9	cis	parietal	SCAN
rs13087788	HIGD1A	cis	cerebellum	SCAN
rs13087788	SNORA62	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43080200-43091000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr3:43085000-43097600	Weak transcription	Ovary	ovary
3	chr3:43085200-43094200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:43088200-43089200	ZNF genes & repeats	Liver	Liver
5	chr3:43088600-43089200	ZNF genes & repeats	Placenta	Placenta
6	chr3:43089000-43089400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet

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