Variant report

Variant	rs2294757
Chromosome Location	chr6:133035098-133035099
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs17604042	0.82[YRI][hapmap]
rs2050153	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2179536	0.82[YRI][hapmap]
rs2223613	0.81[AMR][1000 genomes]
rs2247269	0.84[JPT][hapmap];0.81[AMR][1000 genomes]
rs2247284	0.84[JPT][hapmap];0.81[AMR][1000 genomes]
rs2247285	0.84[JPT][hapmap];0.81[AMR][1000 genomes]
rs2262437	0.84[JPT][hapmap];0.80[AMR][1000 genomes]
rs2262438	0.84[JPT][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes]
rs2300077	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	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2745434	0.82[YRI][hapmap]
rs2745435	0.81[AMR][1000 genomes]
rs2745436	0.84[JPT][hapmap];0.81[AMR][1000 genomes]
rs2745437	0.84[JPT][hapmap];0.81[AMR][1000 genomes]
rs2745439	0.84[JPT][hapmap];0.81[AMR][1000 genomes]
rs2745441	0.84[JPT][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes]
rs2745442	0.84[JPT][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes]
rs2745443	0.84[JPT][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes]
rs2840815	0.84[JPT][hapmap];0.81[AMR][1000 genomes]
rs2840816	0.84[JPT][hapmap];0.81[AMR][1000 genomes]
rs2840817	0.84[JPT][hapmap];0.81[AMR][1000 genomes]
rs2840818	0.81[AMR][1000 genomes]
rs2840820	0.81[MEX][hapmap];0.81[AMR][1000 genomes]
rs2840821	0.84[JPT][hapmap];0.81[AMR][1000 genomes]
rs2840822	0.84[JPT][hapmap];0.81[AMR][1000 genomes]
rs2840823	0.84[JPT][hapmap];0.81[AMR][1000 genomes]
rs2840824	0.81[AMR][1000 genomes]
rs2840825	0.82[AMR][1000 genomes]
rs2840826	0.84[JPT][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes]
rs2840827	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs3798792	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]
rs3798793	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs4897609	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4897610	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4897612	1.00[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.85[TSI][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6936833	0.84[JPT][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes]
rs6938196	0.82[AMR][1000 genomes]
rs6938367	0.82[YRI][hapmap]
rs7742200	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9389027	0.84[JPT][hapmap];0.81[AMR][1000 genomes]
rs9399038	0.84[JPT][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes]
rs990499	0.84[JPT][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes]
rs990500	0.84[JPT][hapmap];0.86[MEX][hapmap];0.82[AMR][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
rs2294757	VNN1	cis	Whole Blood	GTEx
rs2294757	VNN1	cis	lung	GTEx
rs2294757	PDE7B	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:133032800-133035200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr6:133033000-133035200	Active TSS	Liver	Liver
3	chr6:133033200-133035200	Enhancers	Stomach Mucosa	stomach
4	chr6:133033200-133035600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
5	chr6:133033400-133035600	Enhancers	Muscle Satellite Cultured Cells	--
6	chr6:133033600-133035400	Weak transcription	Fetal Intestine Small	intestine
7	chr6:133033600-133035800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr6:133033800-133035200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr6:133033800-133035600	Enhancers	Fetal Intestine Large	intestine
10	chr6:133033800-133035600	Enhancers	HSMM	muscle
11	chr6:133033800-133035600	Enhancers	HSMMtube	muscle
12	chr6:133033800-133036600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr6:133034400-133035200	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr6:133034400-133035200	Enhancers	GM12878-XiMat	blood
15	chr6:133034600-133035600	Enhancers	Primary B cells from peripheral blood	blood
16	chr6:133034600-133035800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr6:133034800-133035200	Flanking Active TSS	Primary B cells from cord blood	blood
18	chr6:133034800-133035200	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr6:133034800-133035200	Enhancers	HepG2	liver
20	chr6:133034800-133035600	Flanking Active TSS	Primary hematopoietic stem cells	blood
21	chr6:133034800-133035600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
22	chr6:133034800-133035600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr6:133034800-133035600	Flanking Active TSS	Duodenum Mucosa	Duodenum
24	chr6:133034800-133053200	Weak transcription	Placenta	Placenta
25	chr6:133035000-133035200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr6:133035000-133035200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:133035000-133035400	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr6:133035000-133035400	Enhancers	Rectal Mucosa Donor 29	rectum

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