Variant report

Variant	rs9504449
Chromosome Location	chr6:5604113-5604114
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1124339	0.83[CEU][hapmap]
rs11755552	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11756138	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs11962015	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[ASN][1000 genomes]
rs11964159	1.00[CHB][hapmap];0.86[GIH][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1546856	1.00[CEU][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs17133295	0.89[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1983564	1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2064106	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2064107	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4323358	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55762144	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56276929	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57607452	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61526984	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6904473	0.93[ASN][1000 genomes]
rs6911625	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6918207	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs6935073	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6936430	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs6942133	0.94[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72817799	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs760676	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs760677	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[LWK][hapmap];1.00[TSI][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]
rs7738833	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7751107	0.93[ASN][1000 genomes]
rs7769150	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs926312	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9328321	0.94[CEU][hapmap];0.93[GIH][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9378434	0.83[CEU][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes]
rs9502321	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9502322	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9504442	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9504443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9504444	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9504445	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9504446	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9504447	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9504448	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9504450	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9504451	0.88[CEU][hapmap];1.00[CHB][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9504452	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9504454	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.97[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	nsv1019428	chr6:5216835-5627839	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv538118	chr6:5216835-5627839	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv916361	chr6:5315853-5695486	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv600887	chr6:5545046-5694713	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1016905	chr6:5566364-5639167	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1015549	chr6:5593965-5630468	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9504449	BMP6	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5577400-5639800	Weak transcription	Fetal Intestine Small	intestine
2	chr6:5581000-5614200	Weak transcription	Lung	lung
3	chr6:5581000-5640400	Weak transcription	Gastric	stomach
4	chr6:5587200-5619400	Weak transcription	Primary B cells from cord blood	blood
5	chr6:5590000-5604400	Weak transcription	Pancreas	Pancrea
6	chr6:5590800-5622000	Weak transcription	Right Atrium	heart
7	chr6:5591200-5619000	Weak transcription	Primary B cells from peripheral blood	blood
8	chr6:5591600-5626400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr6:5591800-5605000	Weak transcription	Primary T cells from cord blood	blood
10	chr6:5592200-5619200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr6:5593200-5604200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:5593400-5621000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:5602600-5605600	Weak transcription	Left Ventricle	heart
14	chr6:5603800-5614000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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