Variant report

Variant	rs2890901
Chromosome Location	chr9:10112766-10112767
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10809027	0.89[CHD][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs10958869	1.00[JPT][hapmap]
rs10958872	0.88[JPT][hapmap]
rs10958873	0.86[JPT][hapmap]
rs10958880	1.00[JPT][hapmap]
rs10958881	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10958888	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10958889	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10958890	1.00[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10958891	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10958892	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10958894	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10958895	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10958896	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10958897	0.80[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10958898	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10958899	0.92[CEU][hapmap];0.89[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10958900	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10958901	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10958902	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10958903	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10958904	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10958905	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10958906	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10958907	1.00[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.93[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10958909	1.00[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];0.96[CHD][hapmap];0.88[JPT][hapmap];0.87[LWK][hapmap];0.92[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10958910	0.92[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10958911	1.00[ASW][hapmap];0.91[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.88[LWK][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap];0.94[ASN][1000 genomes]
rs12004515	0.89[JPT][hapmap]
rs12235311	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12235475	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs12553060	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12555583	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1322159	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.96[ASN][1000 genomes]
rs1322160	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1322161	0.96[ASN][1000 genomes]
rs1567404	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1575260	0.89[CHB][hapmap];0.88[JPT][hapmap];0.85[YRI][hapmap];0.94[ASN][1000 genomes]
rs16931167	0.86[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17618445	0.81[ASN][1000 genomes]
rs1848753	1.00[JPT][hapmap]
rs1848754	1.00[JPT][hapmap]
rs1876854	0.98[ASN][1000 genomes]
rs2197046	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2197048	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2382105	0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2382107	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs35443647	0.89[ASN][1000 genomes]
rs4629932	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs4741010	0.97[ASN][1000 genomes]
rs58750073	0.97[ASN][1000 genomes]
rs66496640	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66585628	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66623460	0.87[ASN][1000 genomes]
rs67153635	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67224985	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67926901	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7037950	0.91[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7043462	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs724231	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs725261	0.89[CHB][hapmap];1.00[CHD][hapmap];0.98[ASN][1000 genomes]
rs725262	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72694843	0.98[ASN][1000 genomes]
rs72694846	0.95[ASN][1000 genomes]
rs7341885	0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7341924	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034731	chr9:9776126-10481262	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv892295	chr9:9832245-10380406	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1021380	chr9:9943339-10126281	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv539989	chr9:9943339-10126281	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv892301	chr9:9971050-10144584	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv892302	chr9:9974221-10158866	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1030657	chr9:10002355-10481262	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv831506	chr9:10040172-10204609	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv824850	chr9:10058091-10134157	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv892304	chr9:10061872-10119157	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv892305	chr9:10061872-10123735	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv892306	chr9:10077180-10127876	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
13	nsv471279	chr9:10081386-10115338	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
14	nsv466156	chr9:10081387-10115338	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	n/a	n/a	inside rSNPs	diseases
15	nsv613373	chr9:10081387-10115338	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
16	nsv892307	chr9:10081387-10123735	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
17	nsv1021508	chr9:10101315-10131581	Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS	n/a	n/a	inside rSNPs	diseases
18	nsv1024401	chr9:10105656-10218577	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
19	nsv539995	chr9:10105656-10218577	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2890901	MORN5	trans	brain	seeQTL
rs2890901	EYA1	trans	brain	seeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:10111800-10114200	Enhancers	Fetal Heart	heart
2	chr9:10111800-10119000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr9:10112000-10112800	Enhancers	Fetal Brain Female	brain
4	chr9:10112400-10113200	Enhancers	Cortex derived primary cultured neurospheres	brain

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