Variant report

Variant	rs2327276
Chromosome Location	chr6:133057017-133057018
allele	A/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	JUN	chr6:133056962-133057162	K562	blood:	n/a	n/a
2	STAT3	chr6:133056992-133057851	MCF10A-Er-Src	breast:	n/a	chr6:133057529-133057543 chr6:133057526-133057546 chr6:133057530-133057541 chr6:133057531-133057540 chr6:133057532-133057541
3	FOXA2	chr6:133055019-133057117	HepG2	liver:	n/a	n/a
4	POLR2A	chr6:133054417-133058306	MCF10A-Er-Src	breast:	n/a	n/a

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
ENSG00000271488	Chromatin interaction
ENSG00000112303	Chromatin interaction
ENSG00000221500	Chromatin interaction
ENSG00000200534	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11752749	0.93[ASN][1000 genomes]
rs12526754	0.81[CHB][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs1883613	0.93[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs1883617	0.93[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs2294758	0.86[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs2294759	0.85[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs2300079	0.93[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs3756974	0.93[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs3813349	0.93[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs4895943	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4897614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56739181	0.92[ASN][1000 genomes]
rs6569828	0.80[CEU][hapmap];0.89[JPT][hapmap]
rs6569832	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6569835	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6569836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6569837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6569839	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6569841	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6569842	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6569843	0.93[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs6569844	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6899338	0.93[ASN][1000 genomes]
rs6899733	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6924414	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6927410	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6935500	0.93[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs6937989	0.92[ASN][1000 genomes]
rs6938188	0.92[ASN][1000 genomes]
rs6942306	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs764263	0.93[ASN][1000 genomes]
rs7752016	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7770949	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9493423	0.93[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs9493425	0.93[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs960711	0.93[CHB][hapmap];0.94[JPT][hapmap];0.93[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
rs2327276	VNN3	cis	Whole Blood	GTEx
rs2327276	VNN2	cis	lung	GTEx
rs2327276	VNN1	cis	Whole Blood	GTEx
rs2327276	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	chr6:133052400-133058800	Enhancers	Stomach Mucosa	stomach
3	chr6:133054400-133058400	Enhancers	HepG2	liver
4	chr6:133055000-133058200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr6:133055200-133057800	Weak transcription	Small Intestine	intestine
6	chr6:133055200-133064800	Weak transcription	Primary T cells from cord blood	blood
7	chr6:133056000-133057200	Weak transcription	Hela-S3	cervix
8	chr6:133056000-133058000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr6:133056000-133058400	Enhancers	Liver	Liver
10	chr6:133056000-133059000	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr6:133056600-133058000	Weak transcription	Placenta	Placenta
12	chr6:133056800-133057400	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr6:133056800-133058000	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr6:133056800-133058200	Weak transcription	Pancreas	Pancrea
15	chr6:133056800-133058600	Enhancers	Primary B cells from cord blood	blood
16	chr6:133056800-133067400	Weak transcription	Primary hematopoietic stem cells	blood

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