Variant report

Variant	rs1984246
Chromosome Location	chr9:15898553-15898554
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 136 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:134)

rs_ID	r²[population]
rs1009468	0.89[CHB][hapmap]
rs10283865	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10733305	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs10738417	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs10738419	0.82[CEU][hapmap];0.91[TSI][hapmap]
rs10756697	0.86[TSI][hapmap]
rs10756704	0.88[TSI][hapmap]
rs10756713	0.80[EUR][1000 genomes]
rs10756714	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs10756715	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs10756717	0.81[EUR][1000 genomes]
rs10756720	0.93[TSI][hapmap]
rs10756724	0.80[CEU][hapmap]
rs10756726	0.85[CEU][hapmap];0.91[TSI][hapmap]
rs10756728	0.86[TSI][hapmap]
rs10756729	0.88[TSI][hapmap]
rs10810438	0.83[CHB][hapmap]
rs10810439	0.81[CEU][hapmap];0.88[TSI][hapmap]
rs10810440	0.80[JPT][hapmap]
rs10810442	0.89[CHB][hapmap]
rs10810455	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs10810461	0.89[CEU][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs10810462	0.88[CEU][hapmap];0.94[EUR][1000 genomes]
rs10810471	0.87[EUR][1000 genomes]
rs10810473	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10810474	0.91[EUR][1000 genomes]
rs10810475	0.89[EUR][1000 genomes]
rs10810479	0.80[CEU][hapmap]
rs10810484	0.84[MEX][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs10810485	0.85[CEU][hapmap]
rs10810488	0.93[TSI][hapmap]
rs10810494	0.86[TSI][hapmap]
rs10810501	0.82[CEU][hapmap]
rs10810502	0.82[CEU][hapmap];0.91[TSI][hapmap]
rs10810506	0.82[CEU][hapmap]
rs10810509	0.82[CEU][hapmap];0.91[TSI][hapmap]
rs10962147	0.89[CHB][hapmap];0.80[JPT][hapmap]
rs10962149	0.89[CHB][hapmap]
rs10962152	0.89[CHB][hapmap]
rs10962153	0.89[CHB][hapmap]
rs10962170	0.89[CHB][hapmap]
rs10962212	0.89[EUR][1000 genomes]
rs10962215	0.89[EUR][1000 genomes]
rs1169478	0.83[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs1169479	0.81[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs1169480	0.89[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs1183919	0.81[ASN][1000 genomes]
rs1328283	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs1328288	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs13292699	0.89[EUR][1000 genomes]
rs1341732	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1341734	0.89[CHB][hapmap];0.80[JPT][hapmap]
rs1355173	0.89[CHB][hapmap];0.80[JPT][hapmap]
rs1359953	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs1396707	0.89[GIH][hapmap];0.86[TSI][hapmap]
rs1396708	0.86[TSI][hapmap]
rs1410444	0.85[CEU][hapmap]
rs1410445	0.80[EUR][1000 genomes]
rs1410446	0.80[EUR][1000 genomes]
rs1410454	0.87[TSI][hapmap]
rs1539171	0.89[CHB][hapmap]
rs1572978	0.89[CHB][hapmap]
rs1891211	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1891212	0.96[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1927697	0.80[EUR][1000 genomes]
rs2066292	0.83[CHB][hapmap]
rs2096121	0.89[CHB][hapmap];0.80[JPT][hapmap]
rs2149231	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs2153725	0.89[CHB][hapmap]
rs2153726	0.89[CHB][hapmap]
rs2153727	0.89[CHB][hapmap]
rs2185665	0.88[CHB][hapmap]
rs2382553	0.89[CHB][hapmap]
rs2382554	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2794634	0.89[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2794636	0.89[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2794645	0.84[ASN][1000 genomes]
rs2794646	0.84[ASN][1000 genomes]
rs2794647	0.82[ASN][1000 genomes]
rs2891007	0.89[CHB][hapmap]
rs2987069	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs2987070	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs2987071	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs2987072	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs3008686	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs4146291	0.88[TSI][hapmap]
rs4472620	0.84[CEU][hapmap]
rs4582646	0.80[EUR][1000 genomes]
rs4740624	0.81[CEU][hapmap];0.88[TSI][hapmap]
rs4740628	0.84[CEU][hapmap];0.92[EUR][1000 genomes]
rs4741534	0.89[GIH][hapmap];0.86[TSI][hapmap]
rs4741535	0.83[TSI][hapmap]
rs4741548	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs4741552	0.86[TSI][hapmap]
rs6474954	0.89[GIH][hapmap];0.86[TSI][hapmap]
rs6474966	0.87[CHB][hapmap];0.80[JPT][hapmap]
rs6474974	0.86[TSI][hapmap]
rs7019205	0.89[CHB][hapmap]
rs7019851	0.89[CHB][hapmap];0.80[JPT][hapmap]
rs7024640	0.86[GIH][hapmap];0.86[TSI][hapmap]
rs7027202	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7032457	0.89[CHB][hapmap]
rs7032634	0.89[CHB][hapmap]
rs7034781	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs7045018	0.89[CHB][hapmap]
rs7047045	0.89[CHB][hapmap]
rs769151	0.91[TSI][hapmap]
rs770191	0.89[CHB][hapmap]
rs770211	0.88[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs770213	0.89[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs770215	0.89[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs7847144	0.89[GIH][hapmap];0.86[TSI][hapmap]
rs7853744	0.89[CHB][hapmap]
rs7866641	0.89[CHB][hapmap]
rs7869624	0.89[CHB][hapmap]
rs7872912	0.89[CHB][hapmap];0.80[JPT][hapmap]
rs9298738	0.89[CHB][hapmap]
rs9298739	0.93[CHB][hapmap]
rs9298740	0.89[CHB][hapmap]
rs9298741	0.89[CHB][hapmap]
rs9406537	0.88[CHB][hapmap]
rs9406542	0.88[CHB][hapmap]
rs9407648	0.88[CHB][hapmap]
rs9407649	0.89[CHB][hapmap]
rs9407650	0.89[CHB][hapmap]
rs9407651	0.89[CHB][hapmap]
rs9407652	0.88[CHB][hapmap]
rs9407654	0.89[CHB][hapmap]
rs9407657	0.89[CHB][hapmap]
rs9407661	0.89[CHB][hapmap]
rs9407662	0.88[CHB][hapmap]
rs961117	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs9650686	0.83[ASN][1000 genomes]
rs9969791	0.82[CEU][hapmap]

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
rs1984246	C9orf93	cis	cerebellum	SCAN
rs1984246	C9orf93	cis	parietal	SCAN

Chromatin state (count:4 , 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	chr9:15897200-15902000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr9:15897800-15901400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr9:15898200-15900800	Weak transcription	Ovary	ovary

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