Variant report

Variant	rs6569843
Chromosome Location	chr6:133061091-133061092
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:133053489..133056295-chr6:133060102..133062322,2	K562	blood:

Variant related genes	Relation type
ENSG00000093134	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10872396	0.83[JPT][hapmap];0.81[AMR][1000 genomes]
rs11752749	0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12526754	0.87[CHB][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883613	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1883617	1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.87[MEX][hapmap];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2267952	0.89[GIH][hapmap];0.81[TSI][hapmap]
rs2294758	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]
rs2294759	0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2300079	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2327276	0.93[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs3756974	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3813349	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.94[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4895943	0.85[GIH][hapmap]
rs4897614	0.93[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs56739181	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6569828	0.84[JPT][hapmap]
rs6569836	0.93[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs6569837	0.93[CHB][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs6569839	0.93[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs6569841	0.94[ASN][1000 genomes]
rs6569842	0.94[ASN][1000 genomes]
rs6899338	0.94[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6924414	0.85[GIH][hapmap]
rs6927410	0.85[GIH][hapmap]
rs6935500	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6937989	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6938188	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6942306	0.87[CHB][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs764263	0.99[ASN][1000 genomes]
rs7752016	0.87[GIH][hapmap]
rs7770949	0.94[ASN][1000 genomes]
rs9493423	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9493425	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs960711	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv965662	chr6:133058111-133063853	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6569843	VNN3	cis	multi-tissue	Pritchard
rs6569843	SNORA33	cis	cerebellum	SCAN
rs6569843	VNN1	cis	Whole Blood	GTEx
rs6569843	VNN3	cis	Whole Blood	GTEx
rs6569843	SCARNA10	trans	parietal	SCAN
rs6569843	VNN2	cis	Whole Blood	GTEx

Chromatin state (count:12 , 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	chr6:133055200-133064800	Weak transcription	Primary T cells from cord blood	blood
3	chr6:133056800-133067400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr6:133057600-133069200	Weak transcription	GM12878-XiMat	blood
5	chr6:133058400-133061800	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr6:133058400-133064800	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr6:133058400-133070400	Weak transcription	Liver	Liver
8	chr6:133058600-133062600	Weak transcription	Primary B cells from cord blood	blood
9	chr6:133058800-133067600	Weak transcription	Placenta	Placenta
10	chr6:133060400-133062200	Weak transcription	Stomach Mucosa	stomach
11	chr6:133060800-133061200	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr6:133061000-133061600	Enhancers	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links