Variant report

Variant	rs4292273
Chromosome Location	chr3:160291431-160291432
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160287495..160289317-chr3:160290381..160292497,2	MCF-7	breast:
2	chr3:160284958..160287547-chr3:160290601..160292287,2	MCF-7	breast:
3	chr3:160281773..160285501-chr3:160290446..160296863,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000186432	Chromatin interaction
ENSG00000229320	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10212236	0.83[EUR][1000 genomes]
rs1451764	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1551190	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1584688	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17236544	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17570467	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1882126	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1882127	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1920642	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1920662	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1920664	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2366969	0.82[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]
rs3732707	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3773372	0.90[EUR][1000 genomes]
rs3851366	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4091703	0.80[EUR][1000 genomes]
rs4292274	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4621370	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4679655	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679888	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4679889	0.81[EUR][1000 genomes]
rs4679890	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4679891	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4679895	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4679896	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4679897	0.82[EUR][1000 genomes]
rs4679899	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4679900	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680587	0.80[EUR][1000 genomes]
rs56197102	0.82[AMR][1000 genomes];0.92[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	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62272794	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62272800	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62272810	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441324	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6768975	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6798668	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6801300	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6806505	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6808083	0.85[ASN][1000 genomes]
rs721023	0.83[EUR][1000 genomes]
rs7618974	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7621724	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7627749	0.83[EUR][1000 genomes]
rs7627756	0.82[EUR][1000 genomes]
rs7634826	0.86[ASN][1000 genomes]
rs7640072	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7643779	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7644453	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7645832	0.83[EUR][1000 genomes]
rs7647873	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9862595	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
5	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
6	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
rs4292273	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160284800-160292000	Weak transcription	Brain Anterior Caudate	brain
2	chr3:160284800-160295000	Weak transcription	Stomach Mucosa	stomach
3	chr3:160284800-160295200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:160285000-160292200	Weak transcription	Primary B cells from cord blood	blood
5	chr3:160285200-160293400	Weak transcription	HepG2	liver
6	chr3:160285200-160294400	Weak transcription	HSMMtube	muscle
7	chr3:160285200-160298800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:160286800-160292800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:160286800-160294800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr3:160286800-160295600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:160286800-160295800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:160286800-160301200	Weak transcription	HMEC	breast
13	chr3:160287000-160292000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:160287000-160292000	Weak transcription	Gastric	stomach
15	chr3:160287000-160293600	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr3:160287000-160295600	Weak transcription	Adipose Nuclei	Adipose
17	chr3:160287200-160291800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr3:160287400-160291800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:160288000-160295400	Weak transcription	Psoas Muscle	Psoas
20	chr3:160288000-160295600	Weak transcription	Liver	Liver
21	chr3:160288200-160295600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr3:160291200-160292200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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