Variant report

Variant	rs7745364
Chromosome Location	chr6:74507729-74507730
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:74502515..74505275-chr6:74506661..74508653,2	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10455097	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10805980	0.95[EUR][1000 genomes]
rs10943125	0.82[AMR][1000 genomes]
rs10943126	0.85[CEU][hapmap];0.87[CHB][hapmap];0.82[AMR][1000 genomes]
rs10943130	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]
rs10943131	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11757360	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12189952	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12209909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12660627	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12663597	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12663978	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1973482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1973483	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2351311	0.92[CEU][hapmap];0.92[MEX][hapmap]
rs4706554	0.87[CHB][hapmap];0.82[GIH][hapmap];0.96[MEX][hapmap];0.82[AMR][1000 genomes]
rs4708084	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4708085	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4708086	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]
rs4708087	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4708089	0.95[MKK][hapmap];0.85[TSI][hapmap]
rs6453696	0.87[EUR][1000 genomes]
rs6903575	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6907989	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6908109	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6909201	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6918540	0.89[EUR][1000 genomes]
rs6924739	0.84[CEU][hapmap]
rs6925924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6939653	0.86[CHB][hapmap];0.82[GIH][hapmap];0.80[AMR][1000 genomes]
rs71309314	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7749499	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7751343	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7751523	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7751558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7751669	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[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]
rs7751758	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7762920	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7763030	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7763254	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7769064	0.91[EUR][1000 genomes]
rs7772434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7773872	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7775539	0.87[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.96[MEX][hapmap];0.80[AMR][1000 genomes]
rs9293942	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9293944	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9343072	0.87[EUR][1000 genomes]
rs9343075	0.88[EUR][1000 genomes]
rs9343078	0.96[CEU][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs9350507	0.89[EUR][1000 genomes]
rs9442959	0.80[AMR][1000 genomes]
rs9442968	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9447004	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.87[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9447013	0.85[EUR][1000 genomes]
rs9447030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs997765	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap]
rs997767	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7745364	COL9A1	cis	parietal	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

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	chr6:74475200-74513600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr6:74476000-74510800	Weak transcription	Fetal Heart	heart
5	chr6:74477400-74543400	Weak transcription	Lung	lung
6	chr6:74484600-74507800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr6:74484600-74508200	Weak transcription	Colon Smooth Muscle	Colon
8	chr6:74484600-74542000	Weak transcription	Right Ventricle	heart
9	chr6:74484800-74508200	Weak transcription	Hela-S3	cervix
10	chr6:74484800-74512600	Weak transcription	HSMM	muscle
11	chr6:74487000-74509600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr6:74489800-74510000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr6:74490200-74508200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr6:74490400-74527800	Weak transcription	Thymus	Thymus
15	chr6:74491600-74508000	Weak transcription	Brain Anterior Caudate	brain
16	chr6:74492400-74510800	Weak transcription	A549	lung
17	chr6:74494400-74510800	Weak transcription	Fetal Lung	lung
18	chr6:74494400-74530800	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr6:74495400-74533200	Weak transcription	Fetal Stomach	stomach
20	chr6:74496800-74528800	Weak transcription	Dnd41	blood
21	chr6:74499000-74527000	Weak transcription	Fetal Thymus	thymus
22	chr6:74499000-74532600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr6:74499200-74520200	Weak transcription	NHEK	skin
24	chr6:74500600-74525800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr6:74500600-74527600	Weak transcription	Primary T cells from cord blood	blood
26	chr6:74501200-74508000	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr6:74501200-74514000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:74501200-74521600	Weak transcription	Fetal Muscle Trunk	muscle
29	chr6:74503200-74520600	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr6:74503400-74520400	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr6:74503400-74521600	Weak transcription	Left Ventricle	heart
32	chr6:74503400-74530600	Weak transcription	Fetal Muscle Leg	muscle
33	chr6:74503600-74520800	Weak transcription	Adipose Nuclei	Adipose
34	chr6:74503800-74508000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr6:74503800-74526600	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr6:74505200-74508200	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr6:74505400-74508400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr6:74505800-74507800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr6:74505800-74509200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr6:74506000-74510000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr6:74506200-74508200	Weak transcription	Brain Hippocampus Middle	brain
42	chr6:74506200-74513600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr6:74506400-74509200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr6:74506600-74508200	Weak transcription	Primary hematopoietic stem cells	blood
45	chr6:74506600-74509200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr6:74506600-74510800	Weak transcription	HUVEC	blood vessel
47	chr6:74506800-74508800	Enhancers	NHDF-Ad	bronchial
48	chr6:74507000-74508000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr6:74507000-74508200	Weak transcription	HMEC	breast
50	chr6:74507000-74508400	Enhancers	NHLF	lung

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