Variant report

Variant	rs17236494
Chromosome Location	chr3:160173600-160173601
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160169346..160171536-chr3:160172001..160174189,2	MCF-7	breast:
2	chr3:160172072..160175654-chr3:160182071..160184575,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000244009	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10923	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10936201	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10936203	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11708118	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11709232	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709336	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11716413	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11719750	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11720689	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11721112	0.81[EUR][1000 genomes]
rs12152435	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12630564	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12630770	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12630956	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12632030	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs12638633	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12639488	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16831207	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17826137	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17826173	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17826257	0.91[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1873076	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1882125	0.82[CHB][hapmap]
rs1920663	0.81[EUR][1000 genomes]
rs2095529	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2099496	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2275151	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3773369	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4679886	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4679892	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4680581	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4680586	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56952700	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60395700	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6441311	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73875254	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73875259	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73875285	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73875290	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7634255	0.82[CHB][hapmap]
rs7644186	0.81[EUR][1000 genomes]

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
rs17236494	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160170200-160175600	Weak transcription	K562	blood
2	chr3:160172800-160174000	Enhancers	Pancreatic Islets	Pancreatic Islet
3	chr3:160173000-160173600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:160173200-160174600	Weak transcription	Brain Anterior Caudate	brain
5	chr3:160173200-160174800	Weak transcription	Brain Hippocampus Middle	brain
6	chr3:160173200-160174800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:160173400-160175400	Weak transcription	Brain Substantia Nigra	brain

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