Variant report

Variant	rs7749493
Chromosome Location	chr6:132175059-132175060
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1044498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11154645	0.82[ASN][1000 genomes]
rs4141767	1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs4897548	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6569761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6569762	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6569763	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6919751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6926728	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6926970	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7767502	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7769712	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs9493113	0.80[ASN][1000 genomes]
rs9493116	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[JPT][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	nsv515476	chr6:131615425-132228577	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv7968	chr6:131917172-132321099	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv886670	chr6:132071193-132193395	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
4	nsv886671	chr6:132071193-132203432	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7749493	VNN1	cis	lymphoblastoid	seeQTL
rs7749493	ENPP1	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:132141000-132176000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:132147600-132199200	Weak transcription	Fetal Stomach	stomach
3	chr6:132151600-132182400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr6:132159600-132176000	Weak transcription	NH-A	brain
5	chr6:132159600-132179800	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr6:132160000-132180600	Weak transcription	Placenta	Placenta
7	chr6:132162200-132211000	Weak transcription	Fetal Kidney	kidney
8	chr6:132162600-132181000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr6:132163000-132181000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr6:132163000-132182600	Weak transcription	HSMMtube	muscle
11	chr6:132163000-132213600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:132163400-132179200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr6:132163600-132183400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr6:132166000-132180000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr6:132166000-132185000	Weak transcription	Fetal Intestine Large	intestine
16	chr6:132166200-132179800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr6:132167400-132176000	Weak transcription	Fetal Muscle Trunk	muscle
18	chr6:132168000-132179200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr6:132168800-132183800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr6:132169800-132181000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr6:132170600-132201800	Weak transcription	Left Ventricle	heart
22	chr6:132170800-132211200	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr6:132171000-132180200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr6:132171200-132183800	Weak transcription	Stomach Mucosa	stomach
25	chr6:132171200-132209400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr6:132172400-132180000	Weak transcription	HSMM	muscle
27	chr6:132172400-132184600	Weak transcription	Fetal Muscle Leg	muscle
28	chr6:132172400-132196800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr6:132172600-132180800	Weak transcription	Aorta	Aorta
30	chr6:132172600-132184600	Weak transcription	Fetal Intestine Small	intestine
31	chr6:132172800-132198200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr6:132173000-132192600	Weak transcription	Adipose Nuclei	Adipose
33	chr6:132173200-132175800	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr6:132173200-132176000	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr6:132173200-132176000	Weak transcription	Osteobl	bone
36	chr6:132173200-132176200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr6:132173200-132176600	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr6:132173200-132181000	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr6:132173400-132176000	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr6:132173400-132176200	Genic enhancers	HepG2	liver
41	chr6:132173800-132179200	Weak transcription	NHLF	lung
42	chr6:132174400-132175200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr6:132175000-132175800	Weak transcription	Liver	Liver

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