Variant report

Variant	rs6789211
Chromosome Location	chr3:160175845-160175846
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10513551	0.85[CEU][hapmap]
rs1317365	0.96[CEU][hapmap];0.81[ASN][1000 genomes]
rs13403	0.85[CEU][hapmap]
rs1451761	0.85[CEU][hapmap]
rs1451762	0.85[CEU][hapmap]
rs1451763	0.84[ASN][1000 genomes]
rs17236544	0.81[CEU][hapmap]
rs17570467	0.81[CEU][hapmap]
rs1882126	0.81[CEU][hapmap]
rs1882127	0.81[CEU][hapmap]
rs1920664	0.81[CEU][hapmap]
rs1953506	0.85[CEU][hapmap]
rs2152425	0.80[CEU][hapmap]
rs2279457	0.85[CEU][hapmap]
rs2305407	0.92[CEU][hapmap]
rs35730266	0.88[ASN][1000 genomes]
rs3773372	0.81[CEU][hapmap]
rs3851366	0.85[CEU][hapmap]
rs4679881	0.85[CEU][hapmap]
rs4679885	0.85[CEU][hapmap]
rs4679890	0.84[CEU][hapmap]
rs4679899	0.82[CEU][hapmap]
rs4680576	0.85[CEU][hapmap]
rs4680579	0.85[CEU][hapmap]
rs4680580	0.85[CEU][hapmap]
rs4680585	0.85[CEU][hapmap]
rs4680588	0.85[CEU][hapmap]
rs6441313	0.85[CEU][hapmap]
rs6441314	0.85[CEU][hapmap]
rs6441319	0.88[CEU][hapmap]
rs6441320	0.85[CEU][hapmap]
rs6768975	0.81[CEU][hapmap]
rs6791261	0.85[CEU][hapmap]
rs6793560	0.84[CEU][hapmap]
rs6798668	0.85[CEU][hapmap]
rs6803828	0.86[CEU][hapmap]
rs6809313	1.00[CEU][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs721022	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs721023	0.85[CEU][hapmap]
rs7611130	0.85[CEU][hapmap]
rs7618974	0.81[CEU][hapmap]
rs7621724	0.82[CEU][hapmap]
rs7624902	0.85[CEU][hapmap]
rs7627756	0.88[CEU][hapmap]
rs7629	0.85[CEU][hapmap]
rs7631792	0.85[CEU][hapmap]
rs7632307	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7634108	0.88[CEU][hapmap]
rs7634826	0.85[CEU][hapmap]
rs7643779	0.81[CEU][hapmap]
rs7647873	0.81[CEU][hapmap]
rs869468	0.85[CEU][hapmap]
rs9862595	0.85[CEU][hapmap]
rs9968151	0.85[CEU][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	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	esv1800136	chr3:159950498-160278160	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	esv1801767	chr3:159950498-160279411	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers 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 miRNA target site	213 gene(s)	inside rSNPs	diseases
6	nsv1008519	chr3:160038710-160292589	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	255 gene(s)	inside rSNPs	diseases
7	esv1801686	chr3:160089896-160248363	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	211 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6789211	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160174800-160176000	Weak transcription	Brain Cingulate Gyrus	brain
2	chr3:160174800-160176600	Enhancers	Brain Hippocampus Middle	brain
3	chr3:160175200-160176400	Enhancers	Brain Angular Gyrus	brain
4	chr3:160175400-160176400	Enhancers	Brain Inferior Temporal Lobe	brain
5	chr3:160175400-160176600	Enhancers	Brain Substantia Nigra	brain
6	chr3:160175600-160178000	Enhancers	K562	blood
7	chr3:160175800-160176400	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:160175800-160179000	Weak transcription	Brain Anterior Caudate	brain

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