Variant report

Variant	rs2745427
Chromosome Location	chr6:133006059-133006060
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:133005010..133007189-chr6:133011041..133014021,2	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1044593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1073954	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12195735	0.82[CEU][hapmap]
rs2050154	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2223613	0.95[CEU][hapmap];0.89[JPT][hapmap];0.89[EUR][1000 genomes]
rs2247269	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs2247284	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs2247285	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs2251449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs2251455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2262437	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs2262438	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs2300077	0.87[CEU][hapmap]
rs2327275	0.89[EUR][1000 genomes]
rs2745426	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2745429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2745430	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2745431	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs2745435	0.89[EUR][1000 genomes]
rs2745436	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs2745437	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs2745439	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs2745440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2745441	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs2745442	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs2745443	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs2745444	0.95[CEU][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2745445	0.94[CEU][hapmap];0.88[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2840812	0.89[ASN][1000 genomes]
rs2840813	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2840815	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs2840816	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs2840817	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs2840818	0.89[EUR][1000 genomes]
rs2840819	0.85[EUR][1000 genomes]
rs2840820	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs2840821	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs2840822	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs2840823	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs2840824	0.89[EUR][1000 genomes]
rs2840825	0.95[CEU][hapmap];0.89[JPT][hapmap];0.89[EUR][1000 genomes]
rs2840826	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs3798792	0.87[CEU][hapmap]
rs3823026	1.00[CEU][hapmap];0.83[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4897600	0.87[EUR][1000 genomes]
rs4897604	0.87[EUR][1000 genomes]
rs4897605	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4897612	0.87[CEU][hapmap]
rs6936833	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs6938196	0.89[EUR][1000 genomes]
rs6941705	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs909975	0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs909977	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9389027	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs9399038	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs990499	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs990500	0.91[CEU][hapmap];0.89[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2745427	VNN1	cis	Whole Blood	GTEx
rs2745427	VNN1	cis	lung	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:133002200-133014600	Strong transcription	Liver	Liver
2	chr6:133003000-133007200	Strong transcription	Duodenum Mucosa	Duodenum
3	chr6:133003000-133008200	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr6:133004200-133006200	Enhancers	NHEK	skin
5	chr6:133004200-133006600	Enhancers	HMEC	breast
6	chr6:133004800-133016400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr6:133005200-133008400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr6:133005200-133008400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr6:133005200-133008800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:133005200-133011000	Weak transcription	Gastric	stomach
11	chr6:133005400-133008400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:133005600-133008400	Weak transcription	HSMM	muscle
13	chr6:133005600-133008400	Weak transcription	Osteobl	bone
14	chr6:133005800-133006600	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr6:133005800-133008400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:133006000-133006200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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