Variant report

Variant	rs1883617
Chromosome Location	chr6:133072650-133072651
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	EP300	chr6:133071838-133072961	GM12878	blood:	n/a	chr6:133071869-133071883
2	NFIC	chr6:133071734-133072896	GM12878	blood:	n/a	chr6:133072178-133072194
3	CUX1	chr6:133072450-133072801	GM12878	blood:	n/a	n/a
4	BHLHE40	chr6:133072533-133072879	GM12878	blood:	n/a	n/a
5	EBF1	chr6:133072481-133072899	GM12878	blood:	n/a	n/a
6	MTA3	chr6:133071734-133072853	GM12878	blood:	n/a	n/a
7	EP300	chr6:133072514-133072868	GM12878	blood:	n/a	n/a
8	BATF	chr6:133072479-133072771	GM12878	blood:	n/a	n/a
9	BATF	chr6:133072412-133072833	GM12878	blood:	n/a	n/a
10	MAX	chr6:133072049-133072895	GM12878	blood:	n/a	n/a
11	JUND	chr6:133071752-133072881	GM12878	blood:	n/a	n/a
12	RUNX3	chr6:133071735-133072917	GM12878	blood:	n/a	n/a
13	NFIC	chr6:133072352-133072837	GM12878	blood:	n/a	n/a
14	RUNX3	chr6:133072370-133072818	GM12878	blood:	n/a	n/a
15	IKZF1	chr6:133071886-133072915	GM12878	blood:	n/a	n/a
16	SPI1	chr6:133072457-133072774	GM12891	blood:	n/a	n/a
17	TBL1XR1	chr6:133071846-133072864	GM12878	blood:	n/a	n/a
18	USF2	chr6:133072553-133072885	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000234484	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10872396	0.87[CEU][hapmap]
rs11752749	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12526754	0.87[CHB][hapmap];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1883613	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2294758	0.92[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2294759	0.94[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2300079	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2327276	0.93[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs3756974	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.88[JPT][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3813349	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.91[LWK][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4897614	0.93[CHB][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs56739181	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6569836	0.93[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs6569837	0.93[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs6569839	0.93[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs6569841	0.87[ASN][1000 genomes]
rs6569842	0.87[ASN][1000 genomes]
rs6569843	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]
rs6899338	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6925157	0.89[GIH][hapmap]
rs6935500	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6937989	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6938188	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6942306	0.87[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs764263	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7770949	0.87[ASN][1000 genomes]
rs9493423	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9493425	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs960711	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[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	nsv517934	chr6:133062916-133072650	Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1883617	VNN1	cis	Whole Blood	GTEx
rs1883617	VNN3	cis	multi-tissue	Pritchard
rs1883617	VNN3	cis	Whole Blood	GTEx
rs1883617	VNN2	Cis_1M	lymphoblastoid	RTeQTL
rs1883617	VNN2	cis	lymphoblastoid	seeQTL
rs1883617	VNN2	cis	multi-tissue	Pritchard
rs1883617	SNORA33	cis	cerebellum	SCAN
rs1883617	VNN2	cis	Whole Blood	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:133061400-133098000	Weak transcription	Spleen	Spleen
2	chr6:133064200-133083000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr6:133064800-133078000	Strong transcription	Primary T cells from cord blood	blood
4	chr6:133065000-133098000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:133065400-133073800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr6:133068800-133083200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr6:133069600-133083200	Weak transcription	Thymus	Thymus
8	chr6:133069800-133075200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr6:133070200-133073800	Genic enhancers	Primary B cells from peripheral blood	blood
10	chr6:133070800-133073000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:133070800-133077600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr6:133070800-133078800	Weak transcription	Placenta	Placenta
13	chr6:133070800-133079000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr6:133071400-133073000	Strong transcription	Primary B cells from cord blood	blood
15	chr6:133071600-133072800	Enhancers	Liver	Liver
16	chr6:133072000-133073400	Flanking Active TSS	GM12878-XiMat	blood
17	chr6:133072000-133073600	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr6:133072000-133076000	Genic enhancers	Primary monocytes fromperipheralblood	blood
19	chr6:133072200-133072800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr6:133072200-133072800	Enhancers	Small Intestine	intestine
21	chr6:133072200-133072800	Enhancers	Stomach Mucosa	stomach
22	chr6:133072200-133073000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
23	chr6:133072200-133073200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr6:133072200-133073200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr6:133072200-133074000	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
26	chr6:133072200-133077200	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
27	chr6:133072200-133079000	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr6:133072400-133072800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
29	chr6:133072400-133073200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr6:133072400-133073200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr6:133072400-133076800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr6:133072600-133072800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr6:133072600-133075400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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