Variant report

Variant	rs1729549
Chromosome Location	chr6:131506165-131506166
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11154621	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11154622	1.00[CHB][hapmap]
rs11755717	1.00[CHB][hapmap]
rs11758994	1.00[CHB][hapmap]
rs1190788	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1190794	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1190796	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1190799	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.84[LWK][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1190800	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1190801	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1190802	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs1190805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1190806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1190809	0.87[EUR][1000 genomes]
rs1190810	0.95[EUR][1000 genomes]
rs1190812	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs1209159	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13195700	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap]
rs13200165	1.00[CHB][hapmap]
rs13206776	1.00[CHB][hapmap]
rs1570348	1.00[CHB][hapmap]
rs1729558	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1746469	0.92[CEU][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs1746470	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[MEX][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1746471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.84[MEX][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1746473	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1746474	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17573187	1.00[CHB][hapmap]
rs17651753	1.00[CHB][hapmap]
rs17787964	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1885641	1.00[CHB][hapmap]
rs3777474	0.92[EUR][1000 genomes]
rs3777476	1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs3777487	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs3903759	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs4310080	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap]
rs4424112	1.00[CHB][hapmap]
rs56318353	1.00[ASN][1000 genomes]
rs66533103	0.81[EUR][1000 genomes]
rs7743894	1.00[CHB][hapmap]
rs9492861	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs9492864	1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs9492865	1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs9492869	1.00[CHB][hapmap]
rs9492874	0.83[ASN][1000 genomes]
rs9492883	1.00[CHB][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1729549	VNN1	cis	cerebellum	SCAN
rs1729549	AKAP7	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131457600-131520800	Weak transcription	Right Ventricle	heart
2	chr6:131458200-131513400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr6:131483000-131506200	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr6:131484400-131509200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr6:131485400-131509600	Weak transcription	Small Intestine	intestine
6	chr6:131485600-131514000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr6:131487000-131512800	Weak transcription	Brain Hippocampus Middle	brain
8	chr6:131488200-131534800	Weak transcription	Gastric	stomach
9	chr6:131489000-131513000	Weak transcription	Colon Smooth Muscle	Colon
10	chr6:131491200-131508000	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr6:131493800-131506600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:131494800-131514000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:131496600-131507200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:131504200-131514000	Weak transcription	Brain Germinal Matrix	brain
15	chr6:131504400-131506600	Strong transcription	Fetal Stomach	stomach
16	chr6:131504600-131506600	Strong transcription	Fetal Intestine Small	intestine
17	chr6:131504600-131507000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr6:131504600-131507000	Weak transcription	NHLF	lung
19	chr6:131504600-131512800	Weak transcription	Brain Angular Gyrus	brain
20	chr6:131504800-131506600	Strong transcription	Fetal Muscle Leg	muscle
21	chr6:131504800-131506600	Strong transcription	Stomach Smooth Muscle	stomach
22	chr6:131504800-131506800	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr6:131504800-131506800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr6:131504800-131507000	Strong transcription	Liver	Liver
25	chr6:131504800-131508000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr6:131505000-131506200	Weak transcription	Primary B cells from cord blood	blood
27	chr6:131505000-131506400	Strong transcription	Placenta	Placenta
28	chr6:131505000-131506600	Strong transcription	Spleen	Spleen
29	chr6:131505000-131506800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr6:131505000-131506800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr6:131505000-131506800	Strong transcription	Adipose Nuclei	Adipose
32	chr6:131505000-131508800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr6:131505000-131512000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr6:131505000-131518800	Weak transcription	Thymus	Thymus
35	chr6:131505000-131521000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr6:131505000-131521800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr6:131505200-131506200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr6:131505200-131506400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr6:131505200-131506400	Strong transcription	Fetal Intestine Large	intestine
40	chr6:131505200-131506600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr6:131505200-131506600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr6:131505200-131506800	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr6:131505200-131507200	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr6:131505200-131507200	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr6:131505200-131507400	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr6:131505200-131507400	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr6:131505200-131507400	Strong transcription	Fetal Lung	lung
48	chr6:131505200-131512800	Weak transcription	Aorta	Aorta
49	chr6:131505200-131513400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr6:131505200-131522600	Weak transcription	HSMMtube	muscle

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