Variant report

Variant	rs4679900
Chromosome Location	chr3:160301772-160301773
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1451764	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1551190	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1584688	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17236544	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17570467	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1882126	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1882127	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1920642	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1920662	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1920664	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28705750	0.81[ASN][1000 genomes]
rs2886825	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3732707	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3773372	0.85[EUR][1000 genomes]
rs3851366	0.87[ASN][1000 genomes]
rs4292273	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4292274	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4621370	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4679655	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679888	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4679890	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4679891	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4679895	0.80[ASN][1000 genomes]
rs4679896	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4679899	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56197102	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56394279	0.85[ASN][1000 genomes]
rs62272791	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62272792	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62272794	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62272800	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62272810	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441324	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6768975	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6798668	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6801300	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6806505	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6808083	0.85[ASN][1000 genomes]
rs7618974	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7621724	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7634826	0.86[ASN][1000 genomes]
rs7640072	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7643779	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7644453	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7647873	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9862595	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv877702	chr3:160262803-160304614	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
5	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
rs4679900	SMC4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160296000-160303000	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr3:160299000-160305000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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