Variant report

Variant	rs2066292
Chromosome Location	chr9:15841937-15841938
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 134 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs1009468	0.83[ASW][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs10283865	0.83[CHB][hapmap]
rs10738415	0.92[ASN][1000 genomes]
rs10756688	0.83[CHB][hapmap]
rs10756689	0.83[CHB][hapmap]
rs10756710	0.80[JPT][hapmap]
rs10756711	0.80[JPT][hapmap]
rs10810438	0.89[CHB][hapmap]
rs10810440	0.89[ASW][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap];0.84[LWK][hapmap]
rs10810442	0.94[CHB][hapmap]
rs1081245	0.97[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10962126	0.82[CHB][hapmap];0.83[LWK][hapmap]
rs10962147	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs10962149	0.94[CHB][hapmap]
rs10962152	0.94[CHB][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes]
rs10962153	0.94[CHB][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes]
rs10962156	0.84[YRI][hapmap];0.81[AFR][1000 genomes]
rs10962170	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs10962173	0.83[ASN][1000 genomes]
rs11515218	0.82[AFR][1000 genomes]
rs11521158	0.82[AFR][1000 genomes]
rs1169478	0.89[CHB][hapmap]
rs1169479	0.94[CHB][hapmap]
rs1169480	0.94[CHB][hapmap]
rs1183919	0.88[AFR][1000 genomes]
rs12341679	0.82[CHB][hapmap]
rs12377371	0.83[CHB][hapmap]
rs12377532	0.92[ASN][1000 genomes]
rs1328288	0.92[CHB][hapmap]
rs1341734	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs1355173	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs1359953	0.94[CHB][hapmap]
rs1396706	0.82[CHB][hapmap]
rs1539171	0.94[CHB][hapmap];0.84[CHD][hapmap]
rs1539173	0.84[YRI][hapmap]
rs1572978	0.94[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1582200	0.87[AFR][1000 genomes]
rs1891211	0.83[CHB][hapmap]
rs1970497	0.81[AFR][1000 genomes]
rs1984246	0.83[CHB][hapmap]
rs2096121	0.94[CHB][hapmap];0.84[JPT][hapmap];0.84[YRI][hapmap]
rs2149231	0.94[CHB][hapmap]
rs2153725	0.94[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs2153726	0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs2153727	0.82[ASW][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs2185665	0.94[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs2382540	0.84[YRI][hapmap]
rs2382553	0.94[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs2794634	0.94[CHB][hapmap]
rs2794636	0.94[CHB][hapmap]
rs2891007	0.94[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs2987069	0.94[CHB][hapmap]
rs2987070	0.94[CHB][hapmap]
rs2987071	0.94[CHB][hapmap]
rs2987072	0.94[CHB][hapmap]
rs3008686	0.94[CHB][hapmap]
rs4741528	0.83[CHB][hapmap]
rs4741546	0.80[JPT][hapmap]
rs6474966	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs7019205	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7019851	0.94[CHB][hapmap];0.81[CHD][hapmap];0.84[JPT][hapmap]
rs7024440	0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7025669	0.83[CHB][hapmap]
rs7027202	0.83[CHB][hapmap]
rs7032457	0.83[ASW][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs7032634	0.94[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs7034484	0.81[CHB][hapmap]
rs7034781	0.89[ASW][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];0.84[JPT][hapmap];0.81[LWK][hapmap]
rs7036674	0.81[CHB][hapmap]
rs7039881	0.88[YRI][hapmap];0.88[AFR][1000 genomes]
rs7045018	0.94[CHB][hapmap]
rs7047045	0.94[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs7388793	0.89[YRI][hapmap];0.87[AFR][1000 genomes]
rs7467156	0.82[CHB][hapmap]
rs7467207	0.81[CHD][hapmap]
rs770191	0.88[ASW][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.80[JPT][hapmap];0.91[LWK][hapmap];0.87[MKK][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs770200	0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs770201	0.89[YRI][hapmap];0.86[AFR][1000 genomes]
rs770205	0.82[YRI][hapmap]
rs770207	0.89[YRI][hapmap];0.87[AFR][1000 genomes]
rs770211	0.94[CHB][hapmap]
rs770213	0.94[CHB][hapmap];0.82[AFR][1000 genomes]
rs770215	0.94[CHB][hapmap]
rs7846970	0.80[AFR][1000 genomes]
rs7853744	0.94[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs7856877	0.86[AFR][1000 genomes]
rs7857126	0.96[ASN][1000 genomes]
rs7860354	0.88[AFR][1000 genomes]
rs7860528	0.89[YRI][hapmap];0.80[AFR][1000 genomes]
rs7860869	0.82[CHB][hapmap]
rs7861802	0.81[AFR][1000 genomes]
rs7866641	0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap]
rs7869624	0.89[ASW][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap];0.88[LWK][hapmap]
rs7872912	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs809493	0.87[AFR][1000 genomes]
rs9298738	0.94[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs9298739	0.93[CHB][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9298740	0.94[CHB][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9298741	0.94[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9406537	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap]
rs9406539	0.89[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9406540	0.95[ASN][1000 genomes]
rs9406541	0.96[ASN][1000 genomes]
rs9406542	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9406545	0.87[ASN][1000 genomes]
rs9407648	0.94[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs9407649	0.94[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs9407650	0.94[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs9407651	0.94[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9407652	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9407653	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9407654	0.94[ASW][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9407655	0.92[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9407656	0.93[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9407657	0.94[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9407658	0.93[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9407660	0.95[ASN][1000 genomes]
rs9407661	0.94[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs9407662	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9407664	0.88[AFR][1000 genomes]
rs9407668	0.86[AFR][1000 genomes]
rs9407669	0.97[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9407671	0.84[YRI][hapmap];0.80[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
3	nsv892632	chr9:15590116-15869845	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv892633	chr9:15604746-15889411	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv892635	chr9:15731775-15876507	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv528964	chr9:15760822-15875162	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv892636	chr9:15794858-15876507	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv613666	chr9:15823667-15875162	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv613667	chr9:15823667-15876507	Enhancers ZNF genes & repeats Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv1016226	chr9:15841107-15875321	ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv1015435	chr9:15841107-15880385	Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2066292	C9orf93	cis	parietal	SCAN
rs2066292	C9orf93	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15830200-15857200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr9:15835000-15846600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr9:15835200-15843400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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