Variant report

Variant	rs7640660
Chromosome Location	chr3:85850041-85850042
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VGLL3-5	chr3:85849953-85850101	ENSG00000241648.1

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11721040	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11926524	0.89[CEU][hapmap]
rs12714637	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs12714640	0.88[CEU][hapmap];1.00[CHD][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13059866	1.00[CHD][hapmap]
rs13068138	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs13078807	0.89[CEU][hapmap];1.00[CHD][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13078960	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs13085840	0.95[EUR][1000 genomes]
rs13096280	1.00[CHD][hapmap]
rs13098327	0.89[CEU][hapmap];0.91[TSI][hapmap]
rs13327074	1.00[CHD][hapmap]
rs1448612	0.89[CEU][hapmap]
rs1597213	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17355368	0.87[CEU][hapmap]
rs2122042	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap]
rs4444725	0.89[CEU][hapmap];0.96[YRI][hapmap]
rs60819488	0.83[AFR][1000 genomes]
rs7355953	1.00[CHD][hapmap]
rs7620339	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap]
rs7622475	0.89[CEU][hapmap];1.00[CHD][hapmap];0.91[TSI][hapmap]
rs7640855	0.89[CEU][hapmap]
rs9309990	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs9309991	0.89[CEU][hapmap];0.95[EUR][1000 genomes]
rs9309994	0.89[CEU][hapmap]
rs9309995	1.00[CHD][hapmap]
rs9818122	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap]
rs9819476	1.00[CHD][hapmap]
rs9820014	0.89[CEU][hapmap]
rs9826482	0.88[CEU][hapmap]
rs9834708	1.00[CHD][hapmap]
rs9837525	0.95[EUR][1000 genomes]
rs9852127	0.86[CEU][hapmap]
rs9852478	0.89[CEU][hapmap]
rs9852859	0.89[CEU][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes]
rs9869320	0.89[CEU][hapmap]
rs9873441	0.92[EUR][1000 genomes]
rs9875880	0.86[EUR][1000 genomes]
rs9877300	1.00[CHD][hapmap]

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	nsv1010541	chr3:85505839-85870597	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv536625	chr3:85505839-85870597	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv532629	chr3:85763873-86608579	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv877106	chr3:85814620-86006210	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv877107	chr3:85814620-86037162	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:85849800-85851400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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