Variant report

Variant	rs742516
Chromosome Location	chr6:133014623-133014624
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs2223613	0.81[ASW][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2247269	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2247284	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2247285	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2251455	0.92[YRI][hapmap]
rs2262437	0.87[AMR][1000 genomes]
rs2262438	0.81[ASW][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2272996	0.82[ASN][1000 genomes]
rs2327275	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2745426	0.82[ASW][hapmap];0.81[LWK][hapmap];0.83[MKK][hapmap];0.93[YRI][hapmap]
rs2745435	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2745436	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2745437	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2745439	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2745441	0.81[ASW][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2745442	0.81[ASW][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2745443	0.86[MEX][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2840815	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2840816	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2840817	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2840818	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2840819	0.83[AMR][1000 genomes]
rs2840820	0.81[ASW][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2840821	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2840822	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2840823	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2840824	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2840825	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2840826	0.86[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2840827	0.85[CEU][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.81[EUR][1000 genomes]
rs3798793	0.85[CEU][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.81[EUR][1000 genomes]
rs4897600	0.85[AMR][1000 genomes]
rs4897604	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4897607	0.81[EUR][1000 genomes]
rs6915807	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6936833	0.86[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6938196	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs909975	0.92[CEU][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs909977	0.82[ASW][hapmap];0.83[MKK][hapmap];0.89[YRI][hapmap]
rs9389027	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9399038	0.86[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs990499	0.86[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs990500	0.86[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.81[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs742516	VNN1	cis	lung	GTEx
rs742516	VNN1	cis	Whole Blood	GTEx
rs742516	VNN1	cis	multi-tissue	Pritchard
rs742516	AHI1	cis	parietal	SCAN
rs742516	PDE7B	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:133004800-133016400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr6:133008800-133016200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr6:133010400-133015200	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr6:133011000-133015200	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr6:133011200-133015000	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr6:133011800-133017200	Weak transcription	Spleen	Spleen
7	chr6:133012600-133015000	Weak transcription	Stomach Mucosa	stomach
8	chr6:133013000-133015000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr6:133013800-133014800	Weak transcription	Duodenum Mucosa	Duodenum
10	chr6:133014200-133014800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:133014200-133015000	Enhancers	Adipose Nuclei	Adipose
12	chr6:133014200-133015000	Enhancers	Pancreas	Pancrea
13	chr6:133014200-133015000	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr6:133014600-133015400	Genic enhancers	Liver	Liver

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