Variant report

Variant	rs6924414
Chromosome Location	chr6:133052384-133052385
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	CEBPB	chr6:133052358-133052517	HepG2	liver:	n/a	n/a
2	ARID3A	chr6:133052343-133052598	HepG2	liver:	n/a	n/a
3	CEBPB	chr6:133051770-133052471	A549	lung:	n/a	n/a
4	POLR2A	chr6:133051597-133052476	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: 4 )

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];0.80[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]
rs4895943	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]
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];0.81[MEX][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];0.81[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]
rs6925157	0.90[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs6927410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[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];0.81[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6924414	VNN1	cis	Whole Blood	GTEx
rs6924414	VNN3	cis	Whole Blood	GTEx
rs6924414	VNN2	cis	Whole Blood	GTEx
rs6924414	VNN3	cis	multi-tissue	Pritchard

Chromatin state (count:20 , 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	chr6:133048400-133052400	Genic enhancers	Primary neutrophils fromperipheralblood	blood
5	chr6:133050000-133052400	Weak transcription	Stomach Mucosa	stomach
6	chr6:133050200-133055600	Weak transcription	NHDF-Ad	bronchial
7	chr6:133050400-133052600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr6:133051200-133052800	Enhancers	NHLF	lung
9	chr6:133051400-133052600	Enhancers	Hela-S3	cervix
10	chr6:133051400-133052800	Enhancers	Pancreatic Islets	Pancreatic Islet
11	chr6:133051600-133052400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr6:133051600-133052400	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr6:133051600-133052600	Enhancers	HepG2	liver
14	chr6:133051600-133052800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:133051600-133053800	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr6:133051800-133052600	Enhancers	Fetal Lung	lung
17	chr6:133052000-133055000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr6:133052000-133055400	Active TSS	Primary B cells from cord blood	blood
19	chr6:133052200-133053000	Flanking Active TSS	Liver	Liver
20	chr6:133052200-133056000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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