Variant report

Variant	rs9343078
Chromosome Location	chr6:74489384-74489385
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10455097	0.96[CEU][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs10805980	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10943125	0.80[EUR][1000 genomes]
rs10943126	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs10943130	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs10943131	0.96[CEU][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs11757360	0.89[EUR][1000 genomes]
rs12189952	0.96[CEU][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs12209909	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs12211905	0.88[EUR][1000 genomes]
rs12660627	0.89[EUR][1000 genomes]
rs12663597	0.89[EUR][1000 genomes]
rs12663978	0.89[EUR][1000 genomes]
rs1973482	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs1973483	0.85[EUR][1000 genomes]
rs2351311	0.87[ASW][hapmap];0.88[CEU][hapmap]
rs4706554	0.80[EUR][1000 genomes]
rs4708084	0.89[EUR][1000 genomes]
rs4708085	0.96[CEU][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes]
rs4708086	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs4708087	0.89[EUR][1000 genomes]
rs4708089	1.00[ASW][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.85[TSI][hapmap];0.90[YRI][hapmap]
rs6453696	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6903575	0.88[EUR][1000 genomes]
rs6907989	0.96[CEU][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs6908109	0.96[CEU][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs6909201	0.96[CEU][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes]
rs6918540	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6924739	0.87[ASW][hapmap];0.88[CEU][hapmap];0.86[MEX][hapmap]
rs6925924	0.88[EUR][1000 genomes]
rs6939653	0.80[EUR][1000 genomes]
rs71309314	0.89[EUR][1000 genomes]
rs7745364	0.96[CEU][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs7749499	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7751343	0.89[EUR][1000 genomes]
rs7751523	0.96[CEU][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs7751558	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs7751669	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs7751758	0.89[EUR][1000 genomes]
rs7762920	0.89[EUR][1000 genomes]
rs7763030	0.89[EUR][1000 genomes]
rs7763254	0.89[EUR][1000 genomes]
rs7769064	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7772434	0.89[EUR][1000 genomes]
rs7773872	0.88[EUR][1000 genomes]
rs7775539	0.80[EUR][1000 genomes]
rs9293942	0.87[EUR][1000 genomes]
rs9293944	0.89[EUR][1000 genomes]
rs9343072	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9343075	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9350507	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9442959	0.80[EUR][1000 genomes]
rs9442968	0.96[CEU][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs9447004	0.96[CEU][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs9447013	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9447030	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs997765	0.96[CEU][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap]
rs997767	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027968	chr6:74155378-74521923	Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
2	nsv538305	chr6:74155378-74521923	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
3	nsv1023250	chr6:74189642-74605976	Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
4	nsv538306	chr6:74189642-74605976	Strong transcription Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
5	nsv463154	chr6:74412048-74775904	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv603695	chr6:74412048-74775904	Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv528148	chr6:74468860-74493432	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9343078	COL9A1	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:74438400-74527200	Weak transcription	Esophagus	oesophagus
2	chr6:74441400-74544400	Weak transcription	Aorta	Aorta
3	chr6:74442400-74493400	Weak transcription	Fetal Muscle Trunk	muscle
4	chr6:74444000-74498600	Weak transcription	Fetal Muscle Leg	muscle
5	chr6:74468000-74492200	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr6:74469800-74502800	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr6:74474000-74489400	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr6:74474800-74498200	Weak transcription	Stomach Smooth Muscle	stomach
9	chr6:74475200-74513600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr6:74476000-74491200	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr6:74476000-74510800	Weak transcription	Fetal Heart	heart
12	chr6:74477400-74543400	Weak transcription	Lung	lung
13	chr6:74480000-74490600	Weak transcription	Primary T cells from cord blood	blood
14	chr6:74480200-74493800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr6:74481800-74490600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr6:74484400-74505800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr6:74484600-74489600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr6:74484600-74490400	Weak transcription	HUVEC	blood vessel
19	chr6:74484600-74490800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr6:74484600-74491400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr6:74484600-74492800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:74484600-74494200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr6:74484600-74495400	Weak transcription	NHEK	skin
24	chr6:74484600-74498000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr6:74484600-74500200	Weak transcription	Left Ventricle	heart
26	chr6:74484600-74507800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:74484600-74508200	Weak transcription	Colon Smooth Muscle	Colon
28	chr6:74484600-74542000	Weak transcription	Right Ventricle	heart
29	chr6:74484800-74489400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:74484800-74490000	Weak transcription	HMEC	breast
31	chr6:74484800-74490600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr6:74484800-74490600	Weak transcription	NHDF-Ad	bronchial
33	chr6:74484800-74491600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr6:74484800-74492200	Weak transcription	A549	lung
35	chr6:74484800-74494000	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr6:74484800-74497800	Weak transcription	Adipose Nuclei	Adipose
37	chr6:74484800-74498600	Weak transcription	NH-A	brain
38	chr6:74484800-74508200	Weak transcription	Hela-S3	cervix
39	chr6:74484800-74512600	Weak transcription	HSMM	muscle
40	chr6:74485000-74489800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr6:74485400-74493400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr6:74485400-74498400	Weak transcription	Osteobl	bone
43	chr6:74486600-74489800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr6:74486800-74490800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr6:74487000-74509600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr6:74488400-74491400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr6:74489000-74489600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr6:74489200-74491000	Enhancers	Liver	Liver

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