Variant report

Variant	rs4895943
Chromosome Location	chr6:133052616-133052617
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:133052448-133052644	MCF10A-Er-Src	breast:	n/a	n/a

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
VNN3	TF binding region
ENSG00000093134	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs11154695	0.84[CHB][hapmap]
rs2267952	0.90[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.81[MEX][hapmap];0.91[ASN][1000 genomes]
rs2300078	0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2327276	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3901670	0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4897614	0.81[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4897615	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6569826	0.88[CEU][hapmap];0.84[GIH][hapmap]
rs6569827	0.88[CEU][hapmap];0.86[GIH][hapmap]
rs6569828	0.84[GIH][hapmap]
rs6569832	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6569835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6569836	0.81[CEU][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6569837	0.81[CEU][hapmap];0.98[GIH][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6569839	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6569841	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6569842	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6569843	0.85[GIH][hapmap]
rs6569844	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6899733	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6924414	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6925157	0.90[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs6927410	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6939079	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6942306	0.81[CEU][hapmap];0.98[GIH][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7752016	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7770949	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9321364	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9493426	0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.83[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
rs4895943	VNN2	cis	Whole Blood	GTEx
rs4895943	VNN3	cis	multi-tissue	Pritchard
rs4895943	VNN1	cis	Whole Blood	GTEx
rs4895943	SLC2A12	cis	cerebellum	SCAN
rs4895943	VNN2	cis	parietal	SCAN
rs4895943	VNN3	cis	Whole Blood	GTEx
rs4895943	C6orf191	cis	parietal	SCAN

Chromatin state (count:19 , 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	chr6:133044400-133066200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr6:133050200-133055600	Weak transcription	NHDF-Ad	bronchial
5	chr6:133051200-133052800	Enhancers	NHLF	lung
6	chr6:133051400-133052800	Enhancers	Pancreatic Islets	Pancreatic Islet
7	chr6:133051600-133052800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:133051600-133053800	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr6:133052000-133055000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr6:133052000-133055400	Active TSS	Primary B cells from cord blood	blood
11	chr6:133052200-133053000	Flanking Active TSS	Liver	Liver
12	chr6:133052200-133056000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr6:133052400-133052800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr6:133052400-133053400	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
15	chr6:133052400-133058800	Enhancers	Stomach Mucosa	stomach
16	chr6:133052600-133054400	Weak transcription	HepG2	liver
17	chr6:133052600-133055000	Weak transcription	Primary T cells from cord blood	blood
18	chr6:133052600-133055600	Weak transcription	Hela-S3	cervix
19	chr6:133052600-133056600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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