Variant report

Variant	rs6899733
Chromosome Location	chr6:133055236-133055237
allele	A/G
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	MYC	chr6:133055023-133055272	MCF10A-Er-Src	breast:	n/a	n/a
2	MAX	chr6:133054960-133055261	NB4	blood:	n/a	n/a
3	STAT3	chr6:133055169-133055274	MCF10A-Er-Src	breast:	n/a	n/a
4	MYC	chr6:133055040-133055309	NB4	blood:	n/a	n/a
5	FOS	chr6:133055004-133055306	MCF10A-Er-Src	breast:	n/a	n/a
6	MYC	chr6:133055000-133055341	MCF10A-Er-Src	breast:	n/a	n/a
7	STAT3	chr6:133055004-133055236	MCF10A-Er-Src	breast:	n/a	n/a
8	STAT3	chr6:133055059-133055344	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr6:133055092-133056842	MCF10A-Er-Src	breast:	n/a	n/a
10	FOXA2	chr6:133055019-133057117	HepG2	liver:	n/a	n/a
11	CEBPB	chr6:133055034-133055322	HepG2	liver:	n/a	chr6:133055152-133055163
12	POLR2A	chr6:133054417-133058306	MCF10A-Er-Src	breast:	n/a	n/a
13	CEBPB	chr6:133055028-133055283	Hela-S3	cervix:	n/a	chr6:133055152-133055163

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:133054032..133057251-chr6:133136548..133139421,3	K562	blood:
2	chr6:133054047..133059196-chr6:133082600..133087082,5	MCF-7	breast:

Variant related genes	Relation type
VNN3	TF binding region
ENSG00000221500	Chromatin interaction
ENSG00000112303	Chromatin interaction
ENSG00000271488	Chromatin interaction
ENSG00000200534	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs2267952	0.91[ASN][1000 genomes]
rs2300078	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2327276	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3901670	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4895943	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4897614	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4897615	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6569832	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6569835	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6569836	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6569837	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6569839	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6569841	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6569842	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6569844	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6924414	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6925157	0.89[ASN][1000 genomes]
rs6927410	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6939079	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6942306	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7752016	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7770949	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9321364	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9493426	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6899733	VNN2	cis	Whole Blood	GTEx
rs6899733	VNN3	cis	Whole Blood	GTEx
rs6899733	VNN1	cis	Whole Blood	GTEx

Chromatin state (count:17 , 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	chr6:133052000-133055400	Active TSS	Primary B cells from cord blood	blood
4	chr6:133052200-133056000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr6:133052400-133058800	Enhancers	Stomach Mucosa	stomach
6	chr6:133052600-133055600	Weak transcription	Hela-S3	cervix
7	chr6:133052600-133056600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr6:133053000-133055800	Active TSS	Liver	Liver
9	chr6:133053400-133056000	Active TSS	Primary hematopoietic stem cells	blood
10	chr6:133053400-133056800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr6:133053800-133056000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
12	chr6:133053800-133056200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr6:133054400-133058400	Enhancers	HepG2	liver
14	chr6:133055000-133058200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr6:133055200-133055400	Enhancers	Placenta	Placenta
16	chr6:133055200-133057800	Weak transcription	Small Intestine	intestine
17	chr6:133055200-133064800	Weak transcription	Primary T cells from cord blood	blood

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