Variant report

Variant	rs9447004
Chromosome Location	chr6:74458737-74458738
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10455097	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10805980	0.86[EUR][1000 genomes]
rs10943125	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10943126	0.85[CEU][hapmap];0.83[CHB][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10943130	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.90[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10943131	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11757360	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12189952	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12209909	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.90[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12211905	0.87[EUR][1000 genomes]
rs12660627	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12663597	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12663978	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13199198	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1973482	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.90[YRI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1973483	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2351311	0.92[CEU][hapmap];0.82[CHD][hapmap];0.96[MEX][hapmap];0.88[AMR][1000 genomes]
rs4706554	0.83[ASW][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4708084	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4708085	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4708086	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.91[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4708087	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6453696	0.94[EUR][1000 genomes]
rs6903575	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6907989	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6908109	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6909201	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6918540	0.92[EUR][1000 genomes]
rs6924739	0.84[CEU][hapmap]
rs6925924	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6939653	0.82[CHB][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71309314	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7745364	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]
rs7749499	1.00[CEU][hapmap];0.90[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7751343	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7751523	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7751558	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.95[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7751669	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7751758	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7762920	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7763030	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7763254	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7769064	0.89[EUR][1000 genomes]
rs7772434	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7773872	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7775539	0.83[ASW][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9293939	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9293942	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9293944	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9343072	0.94[EUR][1000 genomes]
rs9343075	0.93[EUR][1000 genomes]
rs9343078	0.96[CEU][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs9350507	0.91[EUR][1000 genomes]
rs9442959	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9442968	0.88[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];0.91[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9447010	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9447013	0.89[EUR][1000 genomes]
rs9447030	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.91[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs997765	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap]
rs997767	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[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

Variant related diseases (count:1)

Disease	PMID	Source
Calcium levels	24068962	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9447004	COL9A1	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:74414800-74474600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr6:74425200-74475800	Weak transcription	Hela-S3	cervix
3	chr6:74425400-74483200	Weak transcription	A549	lung
4	chr6:74435800-74475400	Weak transcription	Primary T cells from cord blood	blood
5	chr6:74438400-74527200	Weak transcription	Esophagus	oesophagus
6	chr6:74441400-74473200	Weak transcription	HUVEC	blood vessel
7	chr6:74441400-74544400	Weak transcription	Aorta	Aorta
8	chr6:74442200-74473400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr6:74442400-74493400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr6:74443400-74484000	Weak transcription	Left Ventricle	heart
11	chr6:74444000-74498600	Weak transcription	Fetal Muscle Leg	muscle
12	chr6:74444400-74474600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:74448800-74483400	Weak transcription	NHEK	skin
14	chr6:74453600-74479400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr6:74455400-74460000	Weak transcription	Colon Smooth Muscle	Colon
16	chr6:74456000-74461800	Strong transcription	Primary hematopoietic stem cells	blood
17	chr6:74456000-74468400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr6:74456600-74458800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr6:74456800-74461600	Strong transcription	HMEC	breast
20	chr6:74456800-74483800	Weak transcription	NHLF	lung
21	chr6:74457200-74460200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr6:74457200-74472400	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr6:74457200-74484000	Weak transcription	Adipose Nuclei	Adipose
24	chr6:74457400-74465400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr6:74457400-74475400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr6:74457600-74458800	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr6:74457600-74461600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr6:74457600-74469000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr6:74457800-74477600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr6:74458000-74464800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr6:74458200-74458800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr6:74458200-74459200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr6:74458200-74459200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr6:74458400-74460600	Weak transcription	NHDF-Ad	bronchial

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