Variant report

Variant	rs2294758
Chromosome Location	chr6:133045812-133045813
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:133045534..133047240-chr6:133133857..133135793,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112306	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10872396	0.87[CEU][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes]
rs11752749	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12526754	0.81[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1883613	0.92[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1883617	0.92[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2294759	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2300079	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2327276	0.86[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs3756974	0.94[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3813349	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4897614	0.87[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs56739181	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6569828	0.84[JPT][hapmap]
rs6569836	0.87[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs6569837	0.87[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs6569839	0.87[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs6569841	0.89[ASN][1000 genomes]
rs6569842	0.89[ASN][1000 genomes]
rs6569843	0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6899338	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6925157	0.89[GIH][hapmap]
rs6935500	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6937989	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6938188	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6942306	0.81[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs764263	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7770949	0.89[ASN][1000 genomes]
rs9493423	1.00[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9493425	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs960711	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2294758	VNN2	cis	Whole Blood	GTEx
rs2294758	VNN2	Cis_1M	lymphoblastoid	RTeQTL
rs2294758	VNN3	cis	Whole Blood	GTEx
rs2294758	RP1-55C23.7	cis	Whole Blood	GTEx
rs2294758	VNN2	cis	lymphoblastoid	seeQTL
rs2294758	SNORD101	cis	cerebellum	SCAN
rs2294758	VNN1	cis	Whole Blood	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:133034800-133053200	Weak transcription	Placenta	Placenta
2	chr6:133038000-133053400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr6:133041800-133048400	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr6:133043000-133047800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:133043200-133046000	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr6:133043200-133050000	Strong transcription	Liver	Liver
7	chr6:133043200-133051200	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr6:133043600-133051600	Weak transcription	HepG2	liver
9	chr6:133044400-133052000	Weak transcription	Primary B cells from cord blood	blood
10	chr6:133044400-133066200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr6:133045600-133046000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr6:133045800-133046400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links