Variant report

Variant	rs3008714
Chromosome Location	chr9:16015859-16015860
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 152 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:148)

rs_ID	r²[population]
rs1009468	0.88[CHB][hapmap]
rs1080485	0.89[EUR][1000 genomes]
rs10810512	0.84[AMR][1000 genomes]
rs10962251	0.84[AMR][1000 genomes]
rs10962252	0.84[AMR][1000 genomes]
rs1169478	0.89[CEU][hapmap];0.83[CHB][hapmap];0.80[JPT][hapmap]
rs1169479	0.88[CEU][hapmap];0.81[CHB][hapmap];0.80[JPT][hapmap];0.95[TSI][hapmap]
rs1169480	0.88[CEU][hapmap];0.88[CHB][hapmap];0.80[JPT][hapmap]
rs11790527	0.83[AMR][1000 genomes]
rs11792622	0.84[AMR][1000 genomes]
rs1328265	0.95[EUR][1000 genomes]
rs1328269	0.97[EUR][1000 genomes]
rs1328271	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1328286	0.81[CEU][hapmap];0.89[TSI][hapmap]
rs1328288	0.82[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap]
rs13298860	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs13298936	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs1359950	0.87[EUR][1000 genomes]
rs1359951	0.83[EUR][1000 genomes]
rs1359953	0.85[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap]
rs1572978	0.88[CHB][hapmap]
rs1576171	0.96[EUR][1000 genomes]
rs16933965	0.81[AFR][1000 genomes]
rs17352900	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs17353213	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs1891212	0.80[JPT][hapmap]
rs1927699	0.96[EUR][1000 genomes]
rs1927700	0.96[EUR][1000 genomes]
rs1927701	0.96[EUR][1000 genomes]
rs1927702	0.96[EUR][1000 genomes]
rs1984246	0.80[JPT][hapmap]
rs2017943	0.97[EUR][1000 genomes]
rs2066292	0.81[CHB][hapmap]
rs2094522	0.96[EUR][1000 genomes]
rs2149231	0.88[CHB][hapmap];0.89[JPT][hapmap];0.91[EUR][1000 genomes]
rs2153725	0.88[CHB][hapmap]
rs2153726	0.88[CHB][hapmap]
rs2153727	0.88[CHB][hapmap]
rs2185665	0.88[CHB][hapmap]
rs2225181	0.81[CEU][hapmap]
rs2382543	0.96[EUR][1000 genomes]
rs2382544	0.96[EUR][1000 genomes]
rs2382545	0.93[EUR][1000 genomes]
rs2382546	0.85[EUR][1000 genomes]
rs2382547	0.95[EUR][1000 genomes]
rs2382548	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2794634	0.89[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap]
rs2794636	0.92[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap]
rs2860316	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2891007	0.88[CHB][hapmap]
rs2987008	0.86[EUR][1000 genomes]
rs2987009	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs2987010	0.89[CEU][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.90[EUR][1000 genomes]
rs2987011	0.85[CEU][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs2987012	0.85[CEU][hapmap];0.91[EUR][1000 genomes]
rs2987013	0.85[CEU][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs2987014	0.81[CEU][hapmap];0.92[EUR][1000 genomes]
rs2987016	0.97[EUR][1000 genomes]
rs2987017	0.96[EUR][1000 genomes]
rs2987018	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2987019	0.96[EUR][1000 genomes]
rs2987020	0.95[EUR][1000 genomes]
rs2987021	0.96[EUR][1000 genomes]
rs2987022	0.96[EUR][1000 genomes]
rs2987023	0.96[EUR][1000 genomes]
rs2987024	0.96[EUR][1000 genomes]
rs2987025	0.97[EUR][1000 genomes]
rs2987039	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2987041	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2987042	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2987069	0.85[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap]
rs2987070	0.89[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap]
rs2987071	0.96[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap]
rs2987072	0.89[CEU][hapmap];0.88[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.95[TSI][hapmap]
rs2987079	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2987081	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2987086	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2987090	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2987096	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2987098	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2987099	0.92[EUR][1000 genomes]
rs3008666	0.89[EUR][1000 genomes]
rs3008672	0.88[EUR][1000 genomes]
rs3008681	0.85[CEU][hapmap]
rs3008686	0.89[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap]
rs3008710	0.92[EUR][1000 genomes]
rs3008713	0.92[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs3008715	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3008717	0.97[EUR][1000 genomes]
rs3008719	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3008723	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3008726	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3008727	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3008728	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3008729	0.95[EUR][1000 genomes]
rs3008730	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3008732	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3008736	0.96[EUR][1000 genomes]
rs3008739	0.94[EUR][1000 genomes]
rs3008742	0.95[EUR][1000 genomes]
rs3008744	0.94[EUR][1000 genomes]
rs3008745	0.92[EUR][1000 genomes]
rs3008747	0.85[CEU][hapmap];0.92[EUR][1000 genomes]
rs3008748	0.85[CEU][hapmap];0.91[EUR][1000 genomes]
rs3008749	0.85[CEU][hapmap];0.91[EUR][1000 genomes]
rs3008753	0.90[EUR][1000 genomes]
rs3118736	0.96[EUR][1000 genomes]
rs3124461	0.80[EUR][1000 genomes]
rs4442245	0.85[EUR][1000 genomes]
rs4475627	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6474987	0.96[EUR][1000 genomes]
rs6474988	0.96[EUR][1000 genomes]
rs6474989	0.96[EUR][1000 genomes]
rs66532067	0.83[AMR][1000 genomes]
rs7019205	0.88[CHB][hapmap]
rs7023326	0.90[EUR][1000 genomes]
rs7031840	0.82[AMR][1000 genomes]
rs7032457	0.88[CHB][hapmap]
rs7032634	0.88[CHB][hapmap]
rs7040690	0.83[JPT][hapmap]
rs7047045	0.88[CHB][hapmap]
rs723756	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs735962	0.85[CEU][hapmap]
rs770191	0.88[CHB][hapmap];0.87[TSI][hapmap]
rs770211	0.92[CEU][hapmap];0.87[CHB][hapmap];0.84[JPT][hapmap]
rs770213	0.92[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap]
rs770215	0.81[CEU][hapmap];0.88[CHB][hapmap];0.80[JPT][hapmap]
rs7853744	0.88[CHB][hapmap]
rs9298738	0.88[CHB][hapmap]
rs9298739	0.86[CHB][hapmap]
rs9298740	0.88[CHB][hapmap]
rs9298741	0.88[CHB][hapmap]
rs9406542	0.94[CHB][hapmap]
rs9406568	0.85[EUR][1000 genomes]
rs9406569	0.84[EUR][1000 genomes]
rs9406581	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9407648	0.88[CHB][hapmap]
rs9407649	0.88[CHB][hapmap]
rs9407650	0.88[CHB][hapmap]
rs9407651	0.88[CHB][hapmap]
rs9407652	0.94[CHB][hapmap]
rs9407654	0.88[CHB][hapmap]
rs9407657	0.88[CHB][hapmap]
rs9407661	0.88[CHB][hapmap]
rs9407662	0.88[CHB][hapmap]
rs9407697	0.84[EUR][1000 genomes]
rs9407702	0.96[EUR][1000 genomes]
rs9407712	0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv892637	chr9:15926508-16060746	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv949463	chr9:15970668-16377360	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv831521	chr9:15974174-16106565	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3008714	C9orf93	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16013400-16017600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:16013400-16017800	Weak transcription	Osteobl	bone
3	chr9:16014000-16017000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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