Variant report

Variant	rs6441300
Chromosome Location	chr3:100226967-100226968
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10936221	0.89[CHB][hapmap]
rs11719592	0.84[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap]
rs11920006	0.82[JPT][hapmap]
rs11923942	0.82[JPT][hapmap]
rs11927516	0.81[JPT][hapmap]
rs12634317	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs12636452	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs12639465	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs28722928	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs4075020	0.94[CHB][hapmap]
rs4077302	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs4129205	0.80[JPT][hapmap]
rs4132537	0.86[JPT][hapmap]
rs4928048	0.84[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap]
rs4928049	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs4928097	0.82[JPT][hapmap]
rs4928098	0.82[JPT][hapmap]
rs4928110	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs4928111	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs4928112	0.84[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap]
rs56402168	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56779007	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60272820	0.97[ASN][1000 genomes]
rs62276556	0.97[ASN][1000 genomes]
rs62276559	0.97[ASN][1000 genomes]
rs6441308	0.89[CHB][hapmap]
rs6441316	0.84[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs6441328	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs6441329	0.94[CHB][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap]
rs66791174	0.97[ASN][1000 genomes]
rs67600559	0.97[ASN][1000 genomes]
rs6763178	0.82[JPT][hapmap]
rs6763638	0.80[JPT][hapmap]
rs6777810	0.89[CHB][hapmap]
rs6780654	0.89[CHB][hapmap]
rs6792014	0.89[CHB][hapmap]
rs6798264	0.97[ASN][1000 genomes]
rs6799879	0.84[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs6799882	0.84[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap]
rs6799992	0.84[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs6802787	0.84[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap]
rs6807804	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs6808426	0.84[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap]
rs7426815	0.83[CHB][hapmap]
rs7429277	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs7429392	0.94[CHB][hapmap]
rs7430698	0.86[JPT][hapmap]
rs7430715	0.86[JPT][hapmap]
rs7431846	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs7432710	0.80[JPT][hapmap]
rs7433589	0.84[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap]
rs7611100	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs7619507	0.82[JPT][hapmap]
rs7622658	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs7631877	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs7645690	0.94[CHB][hapmap];0.81[JPT][hapmap]
rs7645700	0.94[CHB][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap]
rs7647499	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs7650523	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7653196	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9809934	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs9810780	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9813069	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9819246	0.89[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap]
rs9823159	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs9843498	0.84[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs9851429	0.82[JPT][hapmap]
rs9855549	0.84[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap]
rs9865411	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs9865776	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs9880036	0.81[CHB][hapmap];0.84[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877218	chr3:100176360-100267619	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6441300	IMPG2	cis	cerebellum	SCAN
rs6441300	TFG	cis	multi-tissue	Pritchard
rs6441300	DCBLD2	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100216200-100229000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr3:100225400-100236800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:100225800-100235000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr3:100226800-100227000	ZNF genes & repeats	Pancreas	Pancrea
5	chr3:100226800-100227200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr3:100226800-100227200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:100226800-100227400	ZNF genes & repeats	Aorta	Aorta
8	chr3:100226800-100227600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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