Variant report

Variant	rs2300077
Chromosome Location	chr6:133030492-133030493
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1044593	0.87[CEU][hapmap]
rs1073954	0.80[EUR][1000 genomes]
rs12213507	0.81[MEX][hapmap]
rs2050153	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2223613	0.95[CEU][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2247269	0.96[CEU][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2247284	0.96[CEU][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2247285	0.96[CEU][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2251449	0.87[CEU][hapmap]
rs2251455	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs2262437	0.96[CEU][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2262438	0.96[CEU][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2294757	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2327275	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][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	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2745436	0.96[CEU][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2745437	0.96[CEU][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2745439	0.96[CEU][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2745440	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs2745441	0.96[CEU][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2745442	0.96[CEU][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2745443	0.96[CEU][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2745444	0.95[CEU][hapmap]
rs2745445	0.94[CEU][hapmap];0.85[YRI][hapmap];0.80[EUR][1000 genomes]
rs2840815	0.95[CEU][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2840816	0.96[CEU][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2840817	0.95[CEU][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2840818	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2840819	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2840820	0.96[CEU][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2840821	0.96[CEU][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2840822	0.96[CEU][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2840823	0.96[CEU][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2840824	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2840825	0.95[CEU][hapmap];0.88[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2840826	0.96[CEU][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3798792	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]
rs3823026	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs4897600	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4897601	0.80[AMR][1000 genomes]
rs4897604	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4897605	0.80[EUR][1000 genomes]
rs4897609	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4897610	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4897612	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6936833	0.95[CEU][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6938196	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6941705	0.82[CEU][hapmap]
rs7742200	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs909977	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs9389027	0.96[CEU][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9399038	0.96[CEU][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs990499	0.96[CEU][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs990500	0.96[CEU][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][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
rs2300077	PDE7B	cis	parietal	SCAN
rs2300077	VNN1	cis	Whole Blood	GTEx
rs2300077	VNN1	cis	lung	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:133017800-133032200	Weak transcription	Duodenum Mucosa	Duodenum
2	chr6:133028400-133031400	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr6:133029000-133032200	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr6:133029800-133030800	Enhancers	Placenta	Placenta
5	chr6:133030200-133032200	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr6:133030200-133032400	Weak transcription	Liver	Liver

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