Variant report

Variant	rs9650677
Chromosome Location	chr9:15544388-15544389
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 105 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs1039813	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1039814	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10481557	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10733295	0.81[CEU][hapmap]
rs10738400	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10756670	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10756671	1.00[CEU][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10756672	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10756674	0.92[CEU][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10756676	0.81[EUR][1000 genomes]
rs10756677	0.92[CEU][hapmap];0.87[MEX][hapmap];0.81[EUR][1000 genomes]
rs10756678	0.81[EUR][1000 genomes]
rs10756679	0.88[CEU][hapmap];0.89[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs10756686	0.88[CEU][hapmap]
rs10756687	0.92[CEU][hapmap];0.95[MEX][hapmap];0.81[EUR][1000 genomes]
rs10756688	0.92[CEU][hapmap];0.87[MEX][hapmap]
rs10756689	0.92[CEU][hapmap]
rs10756690	0.92[CEU][hapmap]
rs10756697	0.84[ASW][hapmap];0.89[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.84[TSI][hapmap]
rs10810397	0.81[CEU][hapmap]
rs10810399	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10810400	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10810401	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10810402	0.89[CEU][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs10810408	0.92[CEU][hapmap];0.91[MEX][hapmap];0.81[EUR][1000 genomes]
rs10810416	0.81[CEU][hapmap]
rs10810419	0.81[CEU][hapmap]
rs10810426	0.81[CEU][hapmap]
rs10810427	0.81[CEU][hapmap]
rs10810428	0.92[CEU][hapmap];0.87[MEX][hapmap]
rs10810429	0.81[CEU][hapmap]
rs10962064	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10962065	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10962066	0.92[CEU][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10962070	1.00[ASW][hapmap];0.92[CEU][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.86[TSI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10962072	0.85[EUR][1000 genomes]
rs10962073	0.84[EUR][1000 genomes]
rs10962098	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs10962099	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs10962110	0.89[CEU][hapmap]
rs10962126	0.81[CEU][hapmap]
rs12340969	0.88[CEU][hapmap]
rs13291638	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1355171	0.81[CEU][hapmap]
rs1396707	0.89[CEU][hapmap];0.95[MEX][hapmap]
rs1396708	0.84[ASW][hapmap];0.89[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap]
rs1533040	0.92[CEU][hapmap];0.95[MEX][hapmap];0.81[EUR][1000 genomes]
rs1553728	0.89[CEU][hapmap]
rs169342	0.81[CEU][hapmap]
rs1812686	0.82[EUR][1000 genomes]
rs183928	0.81[CEU][hapmap]
rs2055772	0.92[CEU][hapmap];0.91[MEX][hapmap];0.81[EUR][1000 genomes]
rs2175082	0.85[CEU][hapmap];0.95[MEX][hapmap]
rs2382534	0.89[CEU][hapmap]
rs276435	0.81[CEU][hapmap]
rs276436	0.81[CEU][hapmap]
rs276448	0.81[CEU][hapmap]
rs276449	0.81[CEU][hapmap]
rs276453	0.81[CEU][hapmap]
rs276455	0.81[CEU][hapmap]
rs3955162	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4281189	0.84[EUR][1000 genomes]
rs432452	0.81[CEU][hapmap]
rs442549	0.81[CEU][hapmap]
rs4448380	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs451878	0.81[CEU][hapmap]
rs4740615	0.92[CEU][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4740619	0.92[CEU][hapmap];0.91[MEX][hapmap];0.80[EUR][1000 genomes]
rs4740620	0.81[EUR][1000 genomes]
rs4741510	1.00[ASW][hapmap];0.95[CHB][hapmap];1.00[LWK][hapmap];0.89[AFR][1000 genomes]
rs4741517	0.81[EUR][1000 genomes]
rs4741519	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs4741528	0.92[CEU][hapmap];0.87[MEX][hapmap]
rs4741534	0.89[CEU][hapmap];0.87[MEX][hapmap]
rs4741535	0.88[CEU][hapmap];0.81[TSI][hapmap]
rs6474931	0.92[CEU][hapmap]
rs6474944	0.92[CEU][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs6474945	0.92[CEU][hapmap]
rs6474954	0.89[CEU][hapmap];0.87[MEX][hapmap]
rs7020760	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7020983	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7023275	0.81[CEU][hapmap];0.83[MEX][hapmap]
rs7024640	0.89[CEU][hapmap];0.86[MEX][hapmap]
rs7025669	0.92[CEU][hapmap]
rs7032755	0.85[CEU][hapmap];0.91[MEX][hapmap]
rs7034484	0.80[CEU][hapmap]
rs7035863	0.88[CEU][hapmap]
rs7036172	0.92[CEU][hapmap]
rs7036674	0.91[CEU][hapmap]
rs7044122	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7389629	0.92[CEU][hapmap];0.83[AFR][1000 genomes]
rs770524	0.84[CEU][hapmap]
rs7847144	0.89[CEU][hapmap];0.91[MEX][hapmap]
rs7859780	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs7860623	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7863088	0.92[CEU][hapmap];0.87[MEX][hapmap];0.81[EUR][1000 genomes]
rs7873152	0.81[CEU][hapmap]
rs7874533	0.92[CEU][hapmap];0.87[MEX][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7875367	0.81[CEU][hapmap];0.83[MEX][hapmap]
rs954663	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892625	chr9:15326251-16064850	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv892626	chr9:15389610-15694690	Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv892627	chr9:15397969-15909450	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv892629	chr9:15516375-15634326	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	esv3407839	chr9:15530438-15665653	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9650677	C9orf93	cis	cerebellum	SCAN
rs9650677	C9orf93	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15544000-15551800	Weak transcription	A549	lung

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