Variant report

Variant	rs10958907
Chromosome Location	chr9:10131581-10131582
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 44 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10809027	0.89[CHD][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs10958869	1.00[JPT][hapmap]
rs10958872	0.88[JPT][hapmap]
rs10958873	0.86[JPT][hapmap]
rs10958880	1.00[JPT][hapmap]
rs10958881	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10958888	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10958889	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.99[ASN][1000 genomes]
rs10958890	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10958891	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.99[ASN][1000 genomes]
rs10958892	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10958894	0.99[ASN][1000 genomes]
rs10958895	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10958896	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10958897	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10958898	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10958899	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10958900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10958901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10958902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10958903	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10958904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10958905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10958906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10958909	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];0.88[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10958910	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10958911	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10958916	0.90[CHB][hapmap]
rs12004515	0.89[JPT][hapmap]
rs12235311	0.84[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12235475	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12553060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12555583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1304641	0.81[CHB][hapmap]
rs1322159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1322160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1322161	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1567404	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1575260	1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16931167	0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs16931219	0.81[CHB][hapmap]
rs1848753	1.00[JPT][hapmap]
rs1848754	1.00[JPT][hapmap]
rs1876854	0.94[ASN][1000 genomes]
rs2197046	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2197048	0.91[ASN][1000 genomes]
rs2382105	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2382107	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2382195	0.81[CHB][hapmap]
rs2890901	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]
rs35443647	0.85[ASN][1000 genomes]
rs4629932	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4741010	0.99[ASN][1000 genomes]
rs58750073	0.99[ASN][1000 genomes]
rs66496640	0.94[ASN][1000 genomes]
rs66585628	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66623460	0.89[ASN][1000 genomes]
rs67153635	0.94[ASN][1000 genomes]
rs67224985	0.99[ASN][1000 genomes]
rs67926901	0.99[ASN][1000 genomes]
rs7037950	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7043462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs724231	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs725261	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.97[ASN][1000 genomes]
rs725262	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72694843	0.94[ASN][1000 genomes]
rs72694846	0.91[ASN][1000 genomes]
rs7341885	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7341924	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

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	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	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	nsv466157	chr9:10119504-10170101	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh	n/a	n/a	inside rSNPs	diseases
12	nsv613374	chr9:10119504-10170101	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	n/a	n/a	inside rSNPs	diseases
13	esv2762790	chr9:10131581-10135016	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:44)

SNP	Gene	Cis/trans	Tissue	Source
rs10958907	EGFLAM	trans	brain	seeQTL
rs10958907	TUBA4B	trans	brain	seeQTL
rs10958907	IGSF1	trans	brain	seeQTL
rs10958907	ST6GALNAC2	trans	brain	seeQTL
rs10958907	EFCAB1	trans	brain	seeQTL
rs10958907	SPAG6	trans	brain	seeQTL
rs10958907	LAMB2	trans	brain	seeQTL
rs10958907	SLC47A2	trans	brain	seeQTL
rs10958907	MORN5	trans	brain	seeQTL
rs10958907	STX1A	trans	brain	seeQTL
rs10958907	SNTB1	trans	brain	seeQTL
rs10958907	C1orf88	trans	brain	seeQTL
rs10958907	RNASE4	trans	brain	seeQTL
rs10958907	C8orf84	trans	brain	seeQTL
rs10958907	CCDC81	trans	brain	seeQTL
rs10958907	CLIC6	trans	brain	seeQTL
rs10958907	EPHX2	trans	brain	seeQTL
rs10958907	TMEM99	trans	brain	seeQTL
rs10958907	CCDC37	trans	brain	seeQTL
rs10958907	MTA3	trans	brain	seeQTL
rs10958907	C1orf87	trans	brain	seeQTL
rs10958907	C7orf10	trans	brain	seeQTL
rs10958907	CAPSL	trans	brain	seeQTL
rs10958907	GMPR	trans	brain	seeQTL
rs10958907	EYA1	trans	brain	seeQTL
rs10958907	PCTP	trans	brain	seeQTL
rs10958907	C11orf70	trans	brain	seeQTL
rs10958907	ARMC3	trans	brain	seeQTL
rs10958907	LEPR	trans	brain	seeQTL
rs10958907	TTC18	trans	brain	seeQTL
rs10958907	IRX3	trans	brain	seeQTL
rs10958907	TEKT1	trans	brain	seeQTL
rs10958907	CCDC11	trans	brain	seeQTL
rs10958907	KIF6	trans	brain	seeQTL
rs10958907	PLEKHA7	trans	brain	seeQTL
rs10958907	UACA	trans	brain	seeQTL
rs10958907	C2orf39	trans	brain	seeQTL
rs10958907	PPIC	trans	brain	seeQTL
rs10958907	ZMYND10	trans	brain	seeQTL
rs10958907	ABI3BP	trans	brain	seeQTL
rs10958907	FOLR1	trans	brain	seeQTL
rs10958907	FAM164C	trans	brain	seeQTL
rs10958907	DNAI1	trans	brain	seeQTL
rs10958907	PDGFRL	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:10123200-10135600	Weak transcription	Fetal Heart	heart
2	chr9:10130200-10131600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:10130400-10131800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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