Variant report

Variant	rs6806505
Chromosome Location	chr3:160305648-160305649
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160298872..160300468-chr3:160304100..160306105,2	K562	blood:

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10212236	0.83[EUR][1000 genomes]
rs11706810	0.81[CEU][hapmap]
rs1317365	0.85[CEU][hapmap]
rs13403	0.96[CEU][hapmap]
rs1451761	0.96[CEU][hapmap];0.83[CHB][hapmap]
rs1451762	0.96[CEU][hapmap];0.83[CHB][hapmap]
rs1451764	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1551190	0.81[CEU][hapmap];0.94[CHB][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1584688	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17236544	1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17570467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1882126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1882127	1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1920642	1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1920657	0.83[JPT][hapmap]
rs1920662	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1920664	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2279457	0.96[CEU][hapmap];0.83[CHB][hapmap]
rs2305407	0.92[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap]
rs2366969	0.83[EUR][1000 genomes]
rs28705750	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2886825	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3732706	0.82[CEU][hapmap];0.88[JPT][hapmap]
rs3732707	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3773372	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[EUR][1000 genomes]
rs3851365	0.81[CEU][hapmap];0.88[JPT][hapmap]
rs3851366	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4292273	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4292274	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4621370	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4679655	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679885	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs4679888	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4679889	0.81[EUR][1000 genomes]
rs4679890	0.96[CEU][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4679891	1.00[CEU][hapmap];0.93[CHB][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4679895	0.80[ASN][1000 genomes]
rs4679896	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4679897	0.81[EUR][1000 genomes]
rs4679899	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4679900	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680579	0.96[CEU][hapmap];0.83[CHB][hapmap]
rs4680580	0.96[CEU][hapmap];0.83[CHB][hapmap]
rs4680585	0.96[CEU][hapmap];0.83[CHB][hapmap]
rs4680588	0.96[CEU][hapmap];0.83[CHB][hapmap]
rs56197102	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56394279	0.85[ASN][1000 genomes]
rs58322641	0.82[EUR][1000 genomes]
rs62272791	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62272792	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62272794	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62272800	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62272810	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441319	0.92[CEU][hapmap];0.83[CHB][hapmap]
rs6441320	0.96[CEU][hapmap];0.83[CHB][hapmap]
rs6441324	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6768975	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6793560	0.92[CEU][hapmap];0.84[CHB][hapmap]
rs6798668	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6801300	0.96[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6808083	0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs721022	0.84[CEU][hapmap]
rs721023	0.96[CEU][hapmap];0.94[CHB][hapmap];0.82[EUR][1000 genomes]
rs7611130	0.96[CEU][hapmap];0.83[CHB][hapmap]
rs7618974	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7621724	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7627749	0.82[EUR][1000 genomes]
rs7627756	0.96[CEU][hapmap];0.94[CHB][hapmap];0.82[EUR][1000 genomes]
rs7629	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs7631792	0.96[CEU][hapmap]
rs7634108	0.92[CEU][hapmap]
rs7634826	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7640072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7643779	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7644453	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7645832	0.82[EUR][1000 genomes]
rs7647873	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9862595	0.96[CEU][hapmap];0.94[CHB][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9968151	0.96[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	nsv4089	chr3:160284848-160330024	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6806505	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160304000-160306000	Enhancers	Skeletal Muscle Female	skeletal muscle
2	chr3:160304600-160306000	Enhancers	Skeletal Muscle Male	skeletal muscle
3	chr3:160305400-160306200	Enhancers	Liver	Liver

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