Variant report

Variant	rs7754788
Chromosome Location	chr6:131505531-131505532
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10484765	0.95[JPT][hapmap]
rs1358962	0.95[JPT][hapmap]
rs1729551	0.92[ASN][1000 genomes]
rs1885640	0.84[CHD][hapmap];0.95[JPT][hapmap]
rs3777478	0.86[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs3777480	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs3777483	0.89[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs3822866	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs3850238	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4311533	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4484548	0.83[ASN][1000 genomes]
rs4897505	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs6924196	0.85[CHD][hapmap];0.95[JPT][hapmap]
rs7744734	0.81[ASN][1000 genomes]
rs7755640	0.86[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7761587	0.89[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs7768335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9321277	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9375806	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9398980	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9483237	0.84[ASN][1000 genomes]
rs9483239	0.81[ASN][1000 genomes]
rs9492886	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032955	chr6:131298803-131818502	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv538443	chr6:131298803-131818502	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv830807	chr6:131390952-131581931	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv886664	chr6:131443843-131754930	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7754788	VNN1	cis	cerebellum	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131457600-131505600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:131457600-131520800	Weak transcription	Right Ventricle	heart
3	chr6:131458000-131505600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr6:131458000-131505800	Weak transcription	Duodenum Mucosa	Duodenum
5	chr6:131458200-131513400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr6:131483000-131506200	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr6:131484400-131509200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr6:131485400-131509600	Weak transcription	Small Intestine	intestine
9	chr6:131485600-131514000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr6:131486000-131505600	Weak transcription	HepG2	liver
11	chr6:131486200-131505800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr6:131487000-131512800	Weak transcription	Brain Hippocampus Middle	brain
13	chr6:131488200-131534800	Weak transcription	Gastric	stomach
14	chr6:131489000-131513000	Weak transcription	Colon Smooth Muscle	Colon
15	chr6:131491200-131508000	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr6:131493800-131506600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:131494800-131514000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:131496600-131507200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr6:131499200-131506000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr6:131500000-131505600	Weak transcription	Esophagus	oesophagus
21	chr6:131500200-131505600	Weak transcription	Ovary	ovary
22	chr6:131504200-131514000	Weak transcription	Brain Germinal Matrix	brain
23	chr6:131504400-131506600	Strong transcription	Fetal Stomach	stomach
24	chr6:131504600-131505600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:131504600-131506600	Strong transcription	Fetal Intestine Small	intestine
26	chr6:131504600-131507000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr6:131504600-131507000	Weak transcription	NHLF	lung
28	chr6:131504600-131512800	Weak transcription	Brain Angular Gyrus	brain
29	chr6:131504800-131505600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr6:131504800-131506600	Strong transcription	Fetal Muscle Leg	muscle
31	chr6:131504800-131506600	Strong transcription	Stomach Smooth Muscle	stomach
32	chr6:131504800-131506800	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr6:131504800-131506800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr6:131504800-131507000	Strong transcription	Liver	Liver
35	chr6:131504800-131508000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr6:131505000-131505600	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr6:131505000-131505600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr6:131505000-131505800	Strong transcription	Brain Substantia Nigra	brain
39	chr6:131505000-131505800	Genic enhancers	Pancreas	Pancrea
40	chr6:131505000-131506200	Weak transcription	Primary B cells from cord blood	blood
41	chr6:131505000-131506400	Strong transcription	Placenta	Placenta
42	chr6:131505000-131506600	Strong transcription	Spleen	Spleen
43	chr6:131505000-131506800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr6:131505000-131506800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr6:131505000-131506800	Strong transcription	Adipose Nuclei	Adipose
46	chr6:131505000-131508800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr6:131505000-131512000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr6:131505000-131518800	Weak transcription	Thymus	Thymus
49	chr6:131505000-131521000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr6:131505000-131521800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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