Variant report

Variant	rs2668795
Chromosome Location	chr9:100483916-100483917
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:100458306..100461038-chr9:100482799..100485082,2	MCF-7	breast:
2	chr9:100476626..100478474-chr9:100481765..100484991,3	MCF-7	breast:
3	chr9:100483705..100485931-chr9:100486955..100489222,2	K562	blood:
4	chr9:100481943..100484213-chr9:100684517..100686414,2	MCF-7	breast:
5	chr9:100483705..100485989-chr9:100486600..100490449,4	K562	blood:
6	chr9:100394686..100396632-chr9:100483638..100486483,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136932	Chromatin interaction
ENSG00000136937	Chromatin interaction
ENSG00000136925	Chromatin interaction
ENSG00000136936	Chromatin interaction

Extended variants
information (count: 133 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs10119687	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs1034099	0.82[JPT][hapmap]
rs1034100	0.82[JPT][hapmap]
rs10512254	0.82[JPT][hapmap]
rs1411344	0.82[JPT][hapmap]
rs1543636	0.82[JPT][hapmap]
rs16923041	0.82[JPT][hapmap]
rs16923112	0.82[JPT][hapmap]
rs16923269	0.82[JPT][hapmap]
rs16923677	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs1928641	0.82[JPT][hapmap]
rs1928642	0.82[JPT][hapmap]
rs2244833	0.98[EUR][1000 genomes]
rs2245694	0.83[CHD][hapmap]
rs2282066	0.82[JPT][hapmap]
rs2282067	0.82[JPT][hapmap]
rs2297155	0.82[JPT][hapmap]
rs2297156	0.82[JPT][hapmap]
rs2297157	0.82[JPT][hapmap]
rs2297158	0.82[JPT][hapmap]
rs2297159	0.82[JPT][hapmap]
rs2297160	0.82[JPT][hapmap]
rs2401635	0.82[JPT][hapmap]
rs2668794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2668796	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2668797	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2668799	0.98[EUR][1000 genomes]
rs2668802	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2668803	0.98[EUR][1000 genomes]
rs2668804	0.99[EUR][1000 genomes]
rs2668805	0.98[EUR][1000 genomes]
rs2805768	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2805769	0.95[EUR][1000 genomes]
rs2805770	0.95[EUR][1000 genomes]
rs2805771	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2805773	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2805778	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs2805780	0.99[EUR][1000 genomes]
rs2805781	0.99[EUR][1000 genomes]
rs2805782	0.98[EUR][1000 genomes]
rs2805784	0.99[EUR][1000 genomes]
rs2805789	0.99[EUR][1000 genomes]
rs2805790	0.99[EUR][1000 genomes]
rs2805794	0.99[EUR][1000 genomes]
rs2805795	0.88[EUR][1000 genomes]
rs2805796	0.99[EUR][1000 genomes]
rs2805797	0.99[EUR][1000 genomes]
rs2805798	0.99[EUR][1000 genomes]
rs2805799	0.99[EUR][1000 genomes]
rs2805800	0.99[EUR][1000 genomes]
rs2805809	0.99[EUR][1000 genomes]
rs2805811	0.98[EUR][1000 genomes]
rs2805812	0.98[EUR][1000 genomes]
rs2805813	0.98[EUR][1000 genomes]
rs2805814	0.98[EUR][1000 genomes]
rs2805815	0.98[EUR][1000 genomes]
rs2805816	0.99[EUR][1000 genomes]
rs2805817	0.99[EUR][1000 genomes]
rs2805818	0.98[EUR][1000 genomes]
rs2805820	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2805822	0.98[EUR][1000 genomes]
rs2808681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2808682	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2808684	1.00[EUR][1000 genomes]
rs2808688	0.98[EUR][1000 genomes]
rs2808693	0.98[EUR][1000 genomes]
rs2808695	0.98[EUR][1000 genomes]
rs2808696	0.98[EUR][1000 genomes]
rs2808697	0.98[EUR][1000 genomes]
rs2808698	0.98[EUR][1000 genomes]
rs2808699	0.95[EUR][1000 genomes]
rs2808700	0.95[EUR][1000 genomes]
rs2808702	0.95[EUR][1000 genomes]
rs28403589	0.82[JPT][hapmap]
rs3176628	0.82[JPT][hapmap]
rs3176629	0.82[JPT][hapmap]
rs3176634	0.82[JPT][hapmap]
rs3176637	0.82[JPT][hapmap]
rs3176638	0.82[JPT][hapmap]
rs3176642	0.82[JPT][hapmap]
rs3176644	0.82[JPT][hapmap]
rs3176651	0.82[JPT][hapmap]
rs3176659	0.82[JPT][hapmap]
rs3176668	0.82[JPT][hapmap]
rs3176670	0.82[JPT][hapmap]
rs3176673	0.82[JPT][hapmap]
rs3176675	0.82[JPT][hapmap]
rs3176682	0.82[JPT][hapmap]
rs3176685	0.82[JPT][hapmap]
rs3176688	0.82[JPT][hapmap]
rs3176694	0.82[JPT][hapmap]
rs3176700	0.82[JPT][hapmap]
rs3176703	0.82[JPT][hapmap]
rs3176708	0.82[JPT][hapmap]
rs3176714	0.82[JPT][hapmap]
rs3176720	0.82[JPT][hapmap]
rs3176721	0.82[JPT][hapmap]
rs3176723	0.82[JPT][hapmap]
rs3176724	0.82[JPT][hapmap]
rs3176726	0.82[JPT][hapmap]
rs3176734	0.82[JPT][hapmap]
rs3176740	0.82[JPT][hapmap]
rs3176744	0.82[JPT][hapmap]
rs3176746	0.82[JPT][hapmap]
rs3176751	0.82[JPT][hapmap]
rs3176752	0.82[JPT][hapmap]
rs3750368	0.82[JPT][hapmap]
rs3750369	0.82[JPT][hapmap]
rs3750370	0.82[JPT][hapmap]
rs3763606	0.82[JPT][hapmap]
rs3802472	0.82[JPT][hapmap]
rs3802473	0.82[JPT][hapmap]
rs3802474	0.82[JPT][hapmap]
rs3824494	0.82[JPT][hapmap]
rs4480232	0.90[CHB][hapmap]
rs62560521	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6478304	0.82[JPT][hapmap]
rs7025403	0.82[JPT][hapmap]
rs7036604	0.82[JPT][hapmap]
rs7045160	0.82[JPT][hapmap]
rs7341850	0.82[JPT][hapmap]
rs7864297	0.90[EUR][1000 genomes]
rs7866961	0.82[JPT][hapmap]
rs7867046	0.82[JPT][hapmap]
rs7869683	0.82[JPT][hapmap]
rs7874554	0.99[EUR][1000 genomes]
rs7875449	0.99[EUR][1000 genomes]
rs7875482	0.99[EUR][1000 genomes]
rs953198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9539	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893610	chr9:100324086-100496160	Active TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1043753	chr9:100458109-100599265	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv614934	chr9:100482976-100550253	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2668795	INVS	cis	parietal	SCAN
rs2668795	WNK2	cis	cerebellum	SCAN
rs2668795	FBP1	cis	cerebellum	SCAN
rs2668795	C9orf89	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100483400-100485000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr9:100483400-100485000	Enhancers	HSMMtube	muscle
3	chr9:100483600-100484000	Enhancers	HSMM	muscle

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