Variant report

Variant	rs6935500
Chromosome Location	chr6:133053587-133053588
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	chr6:133051940..133054001-chr6:133054513..133057511,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000093134	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10872396	0.87[CEU][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes]
rs11752749	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12526754	0.88[CHB][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1883613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1883617	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2294758	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]
rs2294759	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2300079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2327276	0.93[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs3756974	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3813349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4897614	0.94[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs56739181	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6569828	0.84[JPT][hapmap]
rs6569836	0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs6569837	0.93[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs6569839	0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs6569841	0.91[ASN][1000 genomes]
rs6569842	0.91[ASN][1000 genomes]
rs6569843	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6899338	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6937989	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6938188	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6942306	0.87[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs764263	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7770949	0.91[ASN][1000 genomes]
rs9493423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9493425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs960711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6935500	VNN2	Cis_1M	lymphoblastoid	RTeQTL
rs6935500	VNN1	cis	Whole Blood	GTEx
rs6935500	VNN3	cis	Whole Blood	GTEx
rs6935500	RP1-55C23.7	cis	Whole Blood	GTEx
rs6935500	VNN2	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:133044400-133066200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr6:133050200-133055600	Weak transcription	NHDF-Ad	bronchial
3	chr6:133051600-133053800	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr6:133052000-133055000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr6:133052000-133055400	Active TSS	Primary B cells from cord blood	blood
6	chr6:133052200-133056000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr6:133052400-133058800	Enhancers	Stomach Mucosa	stomach
8	chr6:133052600-133054400	Weak transcription	HepG2	liver
9	chr6:133052600-133055000	Weak transcription	Primary T cells from cord blood	blood
10	chr6:133052600-133055600	Weak transcription	Hela-S3	cervix
11	chr6:133052600-133056600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:133053000-133055800	Active TSS	Liver	Liver
13	chr6:133053200-133053800	Enhancers	Placenta	Placenta
14	chr6:133053400-133053800	Active TSS	Monocytes-CD14+_RO01746	blood
15	chr6:133053400-133056000	Active TSS	Primary hematopoietic stem cells	blood
16	chr6:133053400-133056800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood

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