Variant report

Variant	rs10810402
Chromosome Location	chr9:15586534-15586535
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 182 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:171)

rs_ID	r²[population]
rs1039813	0.98[EUR][1000 genomes]
rs1039814	0.98[EUR][1000 genomes]
rs10481557	0.96[CEU][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs10733295	0.85[CEU][hapmap];0.85[GIH][hapmap];0.81[TSI][hapmap]
rs10738400	0.84[EUR][1000 genomes]
rs10738402	0.85[EUR][1000 genomes]
rs10738404	0.81[EUR][1000 genomes]
rs10738405	0.81[EUR][1000 genomes]
rs10738406	0.81[EUR][1000 genomes]
rs10756670	0.84[EUR][1000 genomes]
rs10756671	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs10756672	0.86[EUR][1000 genomes]
rs10756674	0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs10756676	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10756677	0.96[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs10756678	0.92[EUR][1000 genomes]
rs10756679	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs10756680	0.90[EUR][1000 genomes]
rs10756686	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs10756687	0.96[CEU][hapmap];0.81[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes]
rs10756688	0.96[CEU][hapmap];0.93[GIH][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes]
rs10756689	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs10756690	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs10756694	0.81[EUR][1000 genomes]
rs10756695	0.80[EUR][1000 genomes]
rs10756697	0.92[CEU][hapmap];0.93[TSI][hapmap]
rs10756704	0.89[CEU][hapmap];0.91[TSI][hapmap]
rs10810399	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs10810400	0.93[EUR][1000 genomes]
rs10810401	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10810405	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10810407	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10810408	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10810409	0.91[EUR][1000 genomes]
rs10810410	0.81[EUR][1000 genomes]
rs10810416	0.85[CEU][hapmap]
rs10810419	0.85[CEU][hapmap]
rs10810426	0.85[CEU][hapmap]
rs10810427	0.85[CEU][hapmap]
rs10810428	0.96[CEU][hapmap];0.91[GIH][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes]
rs10810429	0.85[CEU][hapmap]
rs10810431	0.81[EUR][1000 genomes]
rs10810432	0.81[EUR][1000 genomes]
rs10810433	0.81[EUR][1000 genomes]
rs10810434	0.81[EUR][1000 genomes]
rs10810438	0.82[CEU][hapmap]
rs10810439	0.96[CEU][hapmap];0.91[TSI][hapmap]
rs10810440	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs10810442	0.85[CEU][hapmap]
rs10962064	0.84[EUR][1000 genomes]
rs10962065	0.84[EUR][1000 genomes]
rs10962066	0.96[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs10962070	0.96[CEU][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes]
rs10962072	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10962073	0.94[EUR][1000 genomes]
rs10962098	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs10962099	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs10962110	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs10962126	0.85[CEU][hapmap];0.81[GIH][hapmap];0.81[TSI][hapmap]
rs10962142	0.85[CEU][hapmap]
rs10962149	0.89[CEU][hapmap]
rs10962151	0.89[CEU][hapmap]
rs11789563	0.81[EUR][1000 genomes]
rs12340969	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs12341679	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs12377371	0.82[CEU][hapmap]
rs13291638	0.90[EUR][1000 genomes]
rs1355171	0.85[CEU][hapmap];0.85[GIH][hapmap];0.82[TSI][hapmap]
rs1396707	0.92[CEU][hapmap];0.93[GIH][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes]
rs1396708	0.92[CEU][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs1533040	0.96[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes]
rs1539171	0.81[GIH][hapmap];0.81[TSI][hapmap]
rs1553728	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs169342	0.85[CEU][hapmap]
rs1812686	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs183928	0.85[CEU][hapmap]
rs192466	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2055772	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2136355	0.81[EUR][1000 genomes]
rs2175080	0.81[CEU][hapmap];0.83[GIH][hapmap];0.82[TSI][hapmap]
rs2175082	0.89[CEU][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs2382532	0.81[EUR][1000 genomes]
rs2382534	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs2457265	0.88[ASN][1000 genomes]
rs2663300	0.83[EUR][1000 genomes]
rs276435	0.85[CEU][hapmap]
rs276436	0.85[CEU][hapmap]
rs276444	0.82[EUR][1000 genomes]
rs276448	0.85[CEU][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs276449	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs276453	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs276454	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs276455	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2821545	0.85[CEU][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs3119699	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3955162	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4146290	0.89[CEU][hapmap]
rs4146291	0.89[CEU][hapmap];0.91[TSI][hapmap]
rs4281189	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs432452	0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs433849	0.88[CEU][hapmap];0.85[CHB][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4339736	0.84[EUR][1000 genomes]
rs440229	0.84[EUR][1000 genomes]
rs442549	0.85[CEU][hapmap]
rs4448380	0.96[EUR][1000 genomes]
rs451878	0.85[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap]
rs4740614	0.82[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.81[TSI][hapmap]
rs4740615	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4740618	0.87[EUR][1000 genomes]
rs4740619	0.96[CEU][hapmap];0.98[GIH][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes]
rs4740620	0.92[EUR][1000 genomes]
rs4740621	0.87[EUR][1000 genomes]
rs4740622	0.81[EUR][1000 genomes]
rs4740624	0.96[CEU][hapmap];0.91[TSI][hapmap]
rs4741510	0.89[CEU][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs4741515	0.91[EUR][1000 genomes]
rs4741517	0.92[EUR][1000 genomes]
rs4741519	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs4741520	0.86[EUR][1000 genomes]
rs4741528	0.96[CEU][hapmap];0.95[GIH][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes]
rs4741529	0.89[EUR][1000 genomes]
rs4741534	0.92[CEU][hapmap];0.93[GIH][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes]
rs4741535	0.92[CEU][hapmap];0.91[TSI][hapmap]
rs6474931	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs6474942	0.86[EUR][1000 genomes]
rs6474944	0.96[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs6474945	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs6474951	0.81[CEU][hapmap]
rs6474952	0.81[CEU][hapmap];0.83[GIH][hapmap];0.82[TSI][hapmap]
rs6474953	0.81[EUR][1000 genomes]
rs6474954	0.92[CEU][hapmap];0.93[GIH][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes]
rs6474955	0.81[EUR][1000 genomes]
rs6474966	0.85[CEU][hapmap]
rs7019851	0.81[TSI][hapmap]
rs7020760	0.84[EUR][1000 genomes]
rs7020983	0.85[EUR][1000 genomes]
rs7023275	0.85[CEU][hapmap];0.81[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.83[TSI][hapmap]
rs7024640	0.92[CEU][hapmap];0.91[GIH][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes]
rs7025669	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs7032755	0.89[CEU][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs7032877	0.87[EUR][1000 genomes]
rs7034484	0.84[CEU][hapmap]
rs7034781	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs7035863	0.88[CEU][hapmap]
rs7036172	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs7036674	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs7044122	0.96[EUR][1000 genomes]
rs7045018	0.89[CEU][hapmap]
rs7049101	0.86[EUR][1000 genomes]
rs7049176	0.86[EUR][1000 genomes]
rs7389047	0.89[EUR][1000 genomes]
rs7389629	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs7467156	0.82[CEU][hapmap]
rs7467207	0.82[CEU][hapmap];0.80[TSI][hapmap]
rs770524	0.92[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7847144	0.92[CEU][hapmap];0.93[GIH][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes]
rs7854714	0.84[EUR][1000 genomes]
rs7855235	0.81[EUR][1000 genomes]
rs7859780	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs7860623	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7860869	0.82[CEU][hapmap]
rs7863088	0.96[CEU][hapmap];0.95[GIH][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes]
rs7873152	0.85[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.83[TSI][hapmap]
rs7874533	0.96[CEU][hapmap];0.93[GIH][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs7875367	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9407624	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs950234	0.82[CEU][hapmap]
rs954663	0.85[CEU][hapmap]
rs9650677	0.83[EUR][1000 genomes]
rs9696751	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9886779	0.83[EUR][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	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
6	nsv892630	chr9:15554960-15694690	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1034795	chr9:15565670-15595591	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1028357	chr9:15565670-15622556	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	esv2752286	chr9:15578017-15794897	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv982197	chr9:15579327-15590303	Weak transcription ZNF genes & repeats Enhancers Strong transcription	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv613652	chr9:15579744-15661859	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10810402	C9orf93	cis	parietal	SCAN
rs10810402	C9orf93	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15553800-15592600	Weak transcription	Left Ventricle	heart
2	chr9:15554000-15590200	Weak transcription	Fetal Stomach	stomach
3	chr9:15562200-15588200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr9:15579400-15590200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr9:15580000-15587000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr9:15580000-15587600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr9:15584400-15588600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr9:15586000-15587000	Weak transcription	Fetal Thymus	thymus
9	chr9:15586000-15588200	Weak transcription	Thymus	Thymus

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