Variant report

Variant	rs4741510
Chromosome Location	chr9:15591372-15591373
allele	A/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:86)

rs_ID	r²[population]
rs1039813	0.86[EUR][1000 genomes]
rs1039814	0.87[EUR][1000 genomes]
rs10481557	1.00[ASW][hapmap];0.85[CEU][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];0.91[TSI][hapmap];0.89[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10756670	0.89[AFR][1000 genomes]
rs10756671	0.84[AFR][1000 genomes]
rs10756672	0.89[AFR][1000 genomes]
rs10756674	0.85[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs10756676	0.84[EUR][1000 genomes]
rs10756677	0.85[CEU][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs10756678	0.83[EUR][1000 genomes]
rs10756679	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs10756680	0.81[EUR][1000 genomes]
rs10756686	0.84[CEU][hapmap]
rs10756687	0.85[CEU][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs10756688	0.85[CEU][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs10756689	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs10756690	0.85[CEU][hapmap]
rs10756697	0.84[ASW][hapmap];0.82[CEU][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.88[TSI][hapmap]
rs10756704	0.88[GIH][hapmap];0.86[TSI][hapmap]
rs10810399	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs10810400	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10810401	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs10810402	0.89[CEU][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs10810405	0.82[EUR][1000 genomes]
rs10810408	0.85[CEU][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs10810409	0.82[EUR][1000 genomes]
rs10810428	0.85[CEU][hapmap];0.88[TSI][hapmap]
rs10810439	0.84[ASW][hapmap];0.85[CEU][hapmap];1.00[LWK][hapmap];0.86[TSI][hapmap]
rs10962065	0.89[AFR][1000 genomes]
rs10962066	0.85[CEU][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs10962070	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs10962072	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10962073	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10962098	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs10962099	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs10962110	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs12340969	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs13291638	0.83[EUR][1000 genomes]
rs1396707	0.81[CEU][hapmap];0.88[TSI][hapmap]
rs1396708	0.84[ASW][hapmap];0.81[CEU][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];0.88[TSI][hapmap]
rs1533040	0.85[CEU][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs1553728	0.81[CEU][hapmap]
rs1812686	0.85[EUR][1000 genomes]
rs2055772	0.85[CEU][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs2175082	0.84[TSI][hapmap]
rs2382534	0.81[CEU][hapmap]
rs276454	0.84[CEU][hapmap]
rs2821545	0.80[MEX][hapmap]
rs3119699	0.81[CEU][hapmap]
rs3955162	0.82[EUR][1000 genomes]
rs4146291	0.84[ASW][hapmap];0.88[GIH][hapmap];1.00[LWK][hapmap];0.86[TSI][hapmap]
rs4281189	0.81[EUR][1000 genomes]
rs433849	0.81[CEU][hapmap]
rs4448380	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4740615	0.85[CEU][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs4740619	0.85[CEU][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs4740620	0.83[EUR][1000 genomes]
rs4740624	0.84[ASW][hapmap];0.85[CEU][hapmap];1.00[LWK][hapmap];0.86[TSI][hapmap]
rs4741515	0.83[EUR][1000 genomes]
rs4741517	0.83[EUR][1000 genomes]
rs4741519	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs4741528	0.85[CEU][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs4741529	0.82[EUR][1000 genomes]
rs4741534	0.81[CEU][hapmap];0.88[TSI][hapmap]
rs4741535	0.81[CEU][hapmap];0.88[GIH][hapmap];0.85[TSI][hapmap]
rs6474931	0.85[CEU][hapmap]
rs6474944	0.85[CEU][hapmap];0.91[TSI][hapmap]
rs6474945	0.85[CEU][hapmap]
rs6474954	0.81[CEU][hapmap];0.88[TSI][hapmap]
rs7020983	0.80[AMR][1000 genomes]
rs7024640	0.81[CEU][hapmap];0.88[TSI][hapmap]
rs7025669	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs7032755	0.83[TSI][hapmap]
rs7036172	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs7036674	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs7044122	0.85[EUR][1000 genomes]
rs7389047	0.80[EUR][1000 genomes]
rs7389629	0.85[CEU][hapmap];0.81[JPT][hapmap]
rs770524	0.81[CEU][hapmap]
rs7847144	0.81[CEU][hapmap];0.88[TSI][hapmap]
rs7859780	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs7860623	0.82[EUR][1000 genomes]
rs7863088	0.85[CEU][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs7874533	0.85[CEU][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs9650677	0.89[AFR][1000 genomes]
rs9696751	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
11	nsv613653	chr9:15590116-15668606	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	nsv892631	chr9:15590116-15694690	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4741510	C9orf93	cis	cerebellum	SCAN
rs4741510	C9orf93	cis	parietal	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	chr9:15587000-15620400	Weak transcription	Pancreas	Pancrea
3	chr9:15588400-15597400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr9:15588600-15600800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr9:15588600-15601000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr9:15589200-15609800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr9:15589400-15592200	Weak transcription	Fetal Thymus	thymus
8	chr9:15589400-15610600	Weak transcription	Thymus	Thymus
9	chr9:15591200-15592800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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