Variant report

Variant	rs9388649
Chromosome Location	chr6:128882520-128882521
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 121 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs10872332	0.87[ASN][1000 genomes]
rs11154440	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11753496	0.99[EUR][1000 genomes]
rs11758690	0.99[EUR][1000 genomes]
rs11969975	0.87[ASN][1000 genomes]
rs12176375	0.87[ASN][1000 genomes]
rs12524679	0.90[EUR][1000 genomes]
rs12525214	0.96[EUR][1000 genomes]
rs12526634	1.00[EUR][1000 genomes]
rs12527086	0.85[CEU][hapmap];1.00[EUR][1000 genomes]
rs12527265	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12529229	0.90[EUR][1000 genomes]
rs12529511	0.99[EUR][1000 genomes]
rs12529947	0.90[EUR][1000 genomes]
rs12529948	0.99[EUR][1000 genomes]
rs1341584	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1341585	0.86[CEU][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.96[EUR][1000 genomes]
rs1341588	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1417894	0.87[ASN][1000 genomes]
rs1417895	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs1417896	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1572964	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs17053280	1.00[CHD][hapmap]
rs17055938	1.00[CHB][hapmap]
rs17056043	0.96[EUR][1000 genomes]
rs17461759	0.85[CEU][hapmap]
rs2144376	1.00[CEU][hapmap]
rs62426796	0.89[EUR][1000 genomes]
rs62426798	0.92[EUR][1000 genomes]
rs62426801	0.99[EUR][1000 genomes]
rs62426804	1.00[EUR][1000 genomes]
rs62426805	1.00[EUR][1000 genomes]
rs62426806	1.00[EUR][1000 genomes]
rs62426840	1.00[EUR][1000 genomes]
rs62426841	1.00[EUR][1000 genomes]
rs62426842	1.00[EUR][1000 genomes]
rs62426844	1.00[EUR][1000 genomes]
rs62426845	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62426846	0.96[EUR][1000 genomes]
rs62426847	0.96[EUR][1000 genomes]
rs62426848	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62426849	0.87[EUR][1000 genomes]
rs62426850	0.87[EUR][1000 genomes]
rs62427780	0.85[EUR][1000 genomes]
rs6569533	1.00[ASN][1000 genomes]
rs6569535	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6569536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6916193	1.00[ASN][1000 genomes]
rs6916294	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6919106	0.87[ASN][1000 genomes]
rs6920943	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6923822	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6924111	1.00[ASN][1000 genomes]
rs6935611	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs714782	0.85[EUR][1000 genomes]
rs717617	0.86[CEU][hapmap]
rs7356823	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7454742	0.96[EUR][1000 genomes]
rs7738739	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7745291	1.00[ASN][1000 genomes]
rs7751094	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7751265	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7754729	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7760287	1.00[EUR][1000 genomes]
rs7760330	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7760572	1.00[EUR][1000 genomes]
rs7760682	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7768240	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7773021	0.87[ASN][1000 genomes]
rs9321121	1.00[CHB][hapmap]
rs9321122	0.81[EUR][1000 genomes]
rs9372893	0.87[ASN][1000 genomes]
rs9372894	1.00[ASN][1000 genomes]
rs9375570	1.00[CHB][hapmap]
rs9375572	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs9375575	1.00[ASN][1000 genomes]
rs9375577	0.87[ASN][1000 genomes]
rs9375578	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9375579	0.87[ASN][1000 genomes]
rs9385464	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs9388638	1.00[CHB][hapmap]
rs9388639	0.87[ASN][1000 genomes]
rs9388640	0.87[ASN][1000 genomes]
rs9388645	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs9388646	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs9388647	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9388648	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9388650	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9388651	1.00[ASN][1000 genomes]
rs9388652	1.00[ASN][1000 genomes]
rs9388654	1.00[ASN][1000 genomes]
rs9398873	0.87[ASN][1000 genomes]
rs9398876	0.87[ASN][1000 genomes]
rs9402051	0.87[ASN][1000 genomes]
rs9402052	0.87[ASN][1000 genomes]
rs9402054	0.87[ASN][1000 genomes]
rs9402055	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9402056	0.87[ASN][1000 genomes]
rs9402057	1.00[CHB][hapmap]
rs9482902	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9491960	1.00[CHD][hapmap]
rs9491965	1.00[CHD][hapmap]
rs9491973	1.00[CHD][hapmap]
rs9491990	0.89[ASN][1000 genomes]
rs9491997	1.00[ASN][1000 genomes]
rs9491999	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9492000	0.85[CEU][hapmap];1.00[EUR][1000 genomes]
rs9492001	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];1.00[ASN][1000 genomes]
rs9492002	1.00[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9492003	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9492004	1.00[EUR][1000 genomes]
rs9492005	1.00[EUR][1000 genomes]
rs9492008	1.00[EUR][1000 genomes]
rs9492011	0.97[EUR][1000 genomes]
rs9492017	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs9492018	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033443	chr6:128306654-128899203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv538440	chr6:128306654-128899203	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1020071	chr6:128579774-129048919	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv538441	chr6:128579774-129048919	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv830801	chr6:128878436-129064667	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9388649	SAMD3	cis	parietal	SCAN
rs9388649	C6orf174	cis	parietal	SCAN
rs9388649	RSPO3	cis	cerebellum	SCAN
rs9388649	CHORDC1	trans	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128881600-128882800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr6:128882000-128882600	Enhancers	Fetal Heart	heart
3	chr6:128882000-128882800	Enhancers	HSMM	muscle
4	chr6:128882000-128882800	Enhancers	HSMMtube	muscle
5	chr6:128882200-128882600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr6:128882200-128882800	Enhancers	NHDF-Ad	bronchial
7	chr6:128882400-128890600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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