Variant report

Variant	rs4897612
Chromosome Location	chr6:133035325-133035326
allele	A/C
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	RFX5	chr6:133034994-133035338	HepG2	liver:	n/a	n/a
2	MXI1	chr6:133035322-133035335	GM12878	blood:	n/a	n/a
3	MAX	chr6:133035006-133035362	NB4	blood:	n/a	chr6:133035229-133035239 chr6:133035231-133035240 chr6:133035230-133035240 chr6:133035230-133035241 chr6:133035229-133035242
4	MYC	chr6:133035004-133035392	MCF10A-Er-Src	breast:	n/a	chr6:133035229-133035239 chr6:133035231-133035240 chr6:133035230-133035240 chr6:133035230-133035241 chr6:133035229-133035242
5	MYC	chr6:133035007-133035385	MCF10A-Er-Src	breast:	n/a	chr6:133035229-133035239 chr6:133035231-133035240 chr6:133035230-133035240 chr6:133035230-133035241 chr6:133035229-133035242
6	MYC	chr6:133034915-133035353	NB4	blood:	n/a	chr6:133035229-133035239 chr6:133035231-133035240 chr6:133035230-133035240 chr6:133035230-133035241 chr6:133035229-133035242
7	STAT3	chr6:133034983-133035330	MCF10A-Er-Src	breast:	n/a	n/a
8	MXI1	chr6:133034993-133035375	HepG2	liver:	n/a	chr6:133035230-133035239

Variant related genes	Relation type
VNN1	TF binding region

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1044593	0.87[CEU][hapmap]
rs17604042	1.00[YRI][hapmap]
rs2050153	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2179536	1.00[YRI][hapmap]
rs2223613	0.95[CEU][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2247269	0.96[CEU][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2247284	0.96[CEU][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2247285	0.96[CEU][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2251449	0.87[CEU][hapmap]
rs2251455	0.86[CEU][hapmap]
rs2262437	0.96[CEU][hapmap];0.84[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2262438	0.96[CEU][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2294757	1.00[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.85[TSI][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2300077	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2327275	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2745426	0.87[CEU][hapmap]
rs2745427	0.87[CEU][hapmap]
rs2745429	0.87[CEU][hapmap]
rs2745434	1.00[YRI][hapmap]
rs2745435	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2745436	0.96[CEU][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2745437	0.96[CEU][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2745439	0.96[CEU][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2745440	0.87[CEU][hapmap]
rs2745441	0.96[CEU][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2745442	0.96[CEU][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2745443	0.96[CEU][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2745444	0.95[CEU][hapmap]
rs2745445	0.94[CEU][hapmap]
rs2840815	0.95[CEU][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2840816	0.96[CEU][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2840817	0.95[CEU][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2840818	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2840819	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2840820	0.96[CEU][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2840821	0.96[CEU][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2840822	0.96[CEU][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2840823	0.96[CEU][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2840824	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2840825	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2840826	0.96[CEU][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2840827	1.00[ASW][hapmap];0.82[YRI][hapmap]
rs3798792	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3798793	1.00[ASW][hapmap];0.82[YRI][hapmap]
rs3823026	0.87[CEU][hapmap]
rs4897600	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4897604	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4897609	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4897610	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6936833	0.95[CEU][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6938196	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6938367	1.00[YRI][hapmap]
rs6941705	0.82[CEU][hapmap]
rs7742200	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs909977	0.87[CEU][hapmap]
rs9389027	0.96[CEU][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9399038	0.96[CEU][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs990499	0.96[CEU][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs990500	0.96[CEU][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][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
rs4897612	PDE7B	cis	parietal	SCAN
rs4897612	VNN1	cis	Whole Blood	GTEx
rs4897612	VNN1	cis	lung	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:133033200-133035600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr6:133033400-133035600	Enhancers	Muscle Satellite Cultured Cells	--
3	chr6:133033600-133035400	Weak transcription	Fetal Intestine Small	intestine
4	chr6:133033600-133035800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr6:133033800-133035600	Enhancers	Fetal Intestine Large	intestine
6	chr6:133033800-133035600	Enhancers	HSMM	muscle
7	chr6:133033800-133035600	Enhancers	HSMMtube	muscle
8	chr6:133033800-133036600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:133034600-133035600	Enhancers	Primary B cells from peripheral blood	blood
10	chr6:133034600-133035800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr6:133034800-133035600	Flanking Active TSS	Primary hematopoietic stem cells	blood
12	chr6:133034800-133035600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr6:133034800-133035600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr6:133034800-133035600	Flanking Active TSS	Duodenum Mucosa	Duodenum
15	chr6:133034800-133053200	Weak transcription	Placenta	Placenta
16	chr6:133035000-133035400	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr6:133035000-133035400	Enhancers	Rectal Mucosa Donor 29	rectum
18	chr6:133035200-133035400	Enhancers	Primary B cells from cord blood	blood
19	chr6:133035200-133035600	Flanking Active TSS	Liver	Liver
20	chr6:133035200-133036200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr6:133035200-133038600	Weak transcription	Stomach Mucosa	stomach

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