Variant report

Variant	rs1169479
Chromosome Location	chr9:15895806-15895807
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 99 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs1009468	0.94[CHB][hapmap]
rs10283865	0.81[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs10810438	0.87[CHB][hapmap]
rs10810440	0.87[CHB][hapmap];0.80[JPT][hapmap]
rs10810442	0.94[CHB][hapmap]
rs10962126	0.87[CHB][hapmap]
rs10962147	0.94[CHB][hapmap];0.80[JPT][hapmap]
rs10962149	0.94[CHB][hapmap]
rs10962152	0.94[CHB][hapmap]
rs10962153	0.94[CHB][hapmap]
rs10962170	0.94[CHB][hapmap]
rs1169478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1169480	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1183919	0.92[ASN][1000 genomes]
rs12341679	0.87[CHB][hapmap]
rs12377371	0.81[CHB][hapmap]
rs1328286	0.85[CEU][hapmap];0.91[TSI][hapmap]
rs1328288	0.81[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs1341734	0.94[CHB][hapmap];0.80[JPT][hapmap]
rs1355173	0.94[CHB][hapmap];0.80[JPT][hapmap]
rs1359952	0.82[TSI][hapmap]
rs1359953	0.89[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1396706	0.81[CHB][hapmap]
rs1539171	0.94[CHB][hapmap]
rs1572978	0.94[CHB][hapmap]
rs1891211	0.81[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs1891212	0.88[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs1927696	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs1984246	0.81[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs2066292	0.94[CHB][hapmap]
rs2096121	0.94[CHB][hapmap];0.80[JPT][hapmap]
rs2149231	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs2153725	0.94[CHB][hapmap]
rs2153726	0.94[CHB][hapmap]
rs2153727	0.94[CHB][hapmap]
rs2185665	0.93[CHB][hapmap]
rs2225181	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs2382553	0.94[CHB][hapmap]
rs2794634	0.92[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2794636	0.91[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.84[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2794645	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2794646	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2794647	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2891007	0.94[CHB][hapmap]
rs2987009	0.85[CEU][hapmap]
rs2987011	0.81[CEU][hapmap];0.86[TSI][hapmap]
rs2987012	0.81[CEU][hapmap]
rs2987013	0.81[CEU][hapmap];0.89[TSI][hapmap]
rs2987014	0.84[CEU][hapmap]
rs2987069	0.88[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap]
rs2987070	0.84[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap]
rs2987071	0.92[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs2987072	0.85[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.89[JPT][hapmap];0.91[TSI][hapmap]
rs3008678	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3008681	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs3008686	0.92[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3008747	0.81[CEU][hapmap]
rs3008748	0.81[CEU][hapmap]
rs3008749	0.81[CEU][hapmap]
rs6474966	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs7019205	0.94[CHB][hapmap]
rs7019851	0.94[CHB][hapmap];0.80[JPT][hapmap]
rs7027202	0.81[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7032457	0.94[CHB][hapmap]
rs7032634	0.94[CHB][hapmap]
rs7034781	0.87[CHB][hapmap];0.80[JPT][hapmap]
rs7045018	0.94[CHB][hapmap]
rs7047045	0.94[CHB][hapmap]
rs735962	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs7467156	0.87[CHB][hapmap]
rs7467207	0.81[CHB][hapmap]
rs770191	0.89[CEU][hapmap];0.94[CHB][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs770211	0.96[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs770213	0.96[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs770215	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7853744	0.94[CHB][hapmap]
rs7860869	0.81[CHB][hapmap]
rs7861456	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7866641	0.94[CHB][hapmap]
rs7869624	0.94[CHB][hapmap]
rs7872912	0.94[CHB][hapmap];0.80[JPT][hapmap]
rs9298738	0.94[CHB][hapmap]
rs9298739	0.92[CHB][hapmap]
rs9298740	0.94[CHB][hapmap]
rs9298741	0.94[CHB][hapmap]
rs9406537	0.93[CHB][hapmap]
rs9406542	0.93[CHB][hapmap]
rs9407648	1.00[CHB][hapmap]
rs9407649	0.94[CHB][hapmap]
rs9407650	0.93[CHB][hapmap]
rs9407651	0.94[CHB][hapmap]
rs9407652	0.93[CHB][hapmap]
rs9407654	0.94[CHB][hapmap]
rs9407657	0.94[CHB][hapmap]
rs9407661	0.94[CHB][hapmap]
rs9407662	0.93[CHB][hapmap]
rs9650686	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1169479	C9orf93	cis	cerebellum	SCAN
rs1169479	C9orf93	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15877000-15903400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:15892800-15897200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr9:15893200-15897800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr9:15893400-15897800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr9:15893400-15897800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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