Variant report

Variant	rs3823468
Chromosome Location	chr6:55921936-55921937
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1011277	1.00[CEU][hapmap];0.87[CHB][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs1016719	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1474698	0.85[CEU][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap]
rs1555129	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1555130	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1925145	0.81[CEU][hapmap]
rs1925152	0.85[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap]
rs1925165	0.96[CEU][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap]
rs1925166	1.00[CEU][hapmap];0.87[CHB][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs1925170	0.96[CEU][hapmap]
rs1925174	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap]
rs1925175	1.00[CEU][hapmap];0.87[CHB][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs1998699	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap]
rs1998700	0.96[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs2076473	0.92[CEU][hapmap];0.87[MEX][hapmap]
rs2223598	0.81[CEU][hapmap]
rs2235735	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2397203	1.00[CEU][hapmap]
rs3846919	0.96[CEU][hapmap];0.92[MEX][hapmap]
rs4612164	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs4712120	0.85[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap]
rs4715577	0.96[CEU][hapmap]
rs4715580	1.00[CEU][hapmap];0.87[CHB][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs4715583	0.96[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap]
rs4715584	0.96[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap]
rs4715594	0.81[CEU][hapmap]
rs6920461	0.92[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap]
rs6927562	1.00[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs761104	1.00[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap]
rs761105	1.00[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap]
rs7741903	0.81[CEU][hapmap]
rs7776118	0.82[CEU][hapmap];0.84[JPT][hapmap]
rs926534	1.00[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap]
rs9296823	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9296827	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes]
rs9296831	0.96[CEU][hapmap]
rs9296832	0.85[CEU][hapmap];0.83[JPT][hapmap]
rs9296833	0.81[CEU][hapmap];0.83[JPT][hapmap]
rs9349804	0.85[CEU][hapmap];0.83[JPT][hapmap]
rs9357887	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes]
rs9357893	0.95[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap]
rs9367676	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs9370479	0.96[CEU][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap]
rs9370482	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes]
rs9382578	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9382584	1.00[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap]
rs9396172	0.81[EUR][1000 genomes]
rs9396173	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes]
rs9396175	0.82[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap]
rs9475556	1.00[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs9475558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9475583	0.96[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap]
rs9475641	0.81[CEU][hapmap];0.83[JPT][hapmap]

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	nsv1034037	chr6:55222409-56069600	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv885911	chr6:55789704-56143231	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv526703	chr6:55810482-56023811	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
4	nsv1023687	chr6:55868611-55940255	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
5	nsv1020208	chr6:55870429-55932120	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv538227	chr6:55870429-55932120	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
7	nsv1029182	chr6:55910866-55991956	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3823468	FBXO9	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:55911800-55940800	Weak transcription	Left Ventricle	heart
2	chr6:55916000-55927000	Weak transcription	Fetal Stomach	stomach
3	chr6:55916200-55922200	Weak transcription	Fetal Muscle Trunk	muscle
4	chr6:55916200-55923400	Weak transcription	Fetal Heart	heart
5	chr6:55920200-55926200	Strong transcription	Fetal Lung	lung
6	chr6:55920600-55928400	Weak transcription	Aorta	Aorta
7	chr6:55920600-56018400	Weak transcription	Ovary	ovary
8	chr6:55921000-55929200	Weak transcription	Right Ventricle	heart
9	chr6:55921000-55930000	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr6:55921800-55922200	Strong transcription	Stomach Smooth Muscle	stomach
11	chr6:55921800-55922600	Strong transcription	Fetal Muscle Leg	muscle
12	chr6:55921800-55928000	Weak transcription	Psoas Muscle	Psoas

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