Variant report

Variant	rs3798792
Chromosome Location	chr6:133032759-133032760
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1044593	0.87[CEU][hapmap]
rs1073954	0.80[EUR][1000 genomes]
rs2050153	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2223613	0.95[CEU][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2247269	0.95[CEU][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2247284	0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2247285	0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2251449	0.87[CEU][hapmap]
rs2251455	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs2262437	0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2262438	0.95[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2267951	0.81[ASN][1000 genomes]
rs2294757	0.89[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.85[TSI][hapmap];0.89[AMR][1000 genomes]
rs2300077	1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2327275	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2745426	0.87[CEU][hapmap]
rs2745427	0.87[CEU][hapmap]
rs2745429	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs2745430	0.80[EUR][1000 genomes]
rs2745435	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2745436	0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2745437	0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2745439	0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2745440	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs2745441	0.95[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2745442	0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2745443	0.95[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2745444	0.95[CEU][hapmap]
rs2745445	0.94[CEU][hapmap];0.80[EUR][1000 genomes]
rs2840815	0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2840816	0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2840817	0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2840818	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2840819	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2840820	0.95[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2840821	0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2840822	0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2840823	0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2840824	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2840825	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2840826	0.95[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3823026	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs4897600	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4897601	0.82[AMR][1000 genomes]
rs4897604	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4897605	0.80[EUR][1000 genomes]
rs4897609	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4897610	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4897612	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6930032	0.80[ASN][1000 genomes]
rs6936833	0.95[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6938196	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6941705	0.82[CEU][hapmap]
rs7742200	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs909977	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs9375912	0.81[ASN][1000 genomes]
rs9389027	0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9399038	0.95[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs990499	0.95[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs990500	0.95[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532069	chr6:132776411-133462292	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv1015742	chr6:132933666-133285852	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3798792	VNN1	cis	lung	GTEx
rs3798792	VNN1	cis	Whole Blood	GTEx
rs3798792	PDE7B	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:133030800-133034400	Weak transcription	Placenta	Placenta
2	chr6:133031800-133033200	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr6:133032200-133033600	Enhancers	Monocytes-CD14+_RO01746	blood
4	chr6:133032200-133034600	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr6:133032400-133032800	Flanking Active TSS	Duodenum Mucosa	Duodenum
6	chr6:133032400-133033000	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr6:133032400-133034600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr6:133032600-133033000	Flanking Active TSS	Liver	Liver
9	chr6:133032600-133033600	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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