Variant report

Variant	rs1920642
Chromosome Location	chr3:160293719-160293720
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160293262..160295786-chr3:160297388..160301495,3	K562	blood:
2	chr3:160284601..160286710-chr3:160293611..160295501,2	MCF-7	breast:
3	chr3:160281773..160285501-chr3:160290446..160296863,5	MCF-7	breast:
4	chr3:160292624..160294762-chr3:160297394..160300194,2	K562	blood:
5	chr3:160291959..160293841-chr3:160293895..160296862,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000186432	Chromatin interaction
ENSG00000229320	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10212236	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11706810	0.81[CEU][hapmap]
rs1317365	0.85[CEU][hapmap]
rs13403	0.96[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs1451761	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs1451762	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs1451764	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1551190	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1584688	0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17236473	0.84[JPT][hapmap]
rs17236544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17570467	1.00[CEU][hapmap];0.94[CHB][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1882126	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1882127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1920662	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1920664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2279457	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2305407	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs2366969	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28705750	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2886825	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3732706	0.82[CEU][hapmap]
rs3732707	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3773372	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3851365	0.81[CEU][hapmap]
rs3851366	0.96[CEU][hapmap];0.82[CHB][hapmap];0.80[EUR][1000 genomes]
rs4091703	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4292273	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4292274	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4621370	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679655	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4679885	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4679888	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4679889	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4679890	0.96[CEU][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4679891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4679896	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4679897	0.82[EUR][1000 genomes]
rs4679899	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679900	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4680579	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs4680580	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs4680585	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4680587	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4680588	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs56197102	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58322641	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60460891	0.85[ASN][1000 genomes]
rs62272791	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62272792	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62272794	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62272800	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62272810	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6441319	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs6441320	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6441324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6768975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6793560	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs6798668	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[EUR][1000 genomes]
rs6801300	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6806505	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6808083	0.83[CHB][hapmap]
rs721022	0.84[CEU][hapmap]
rs721023	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7611130	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs7618974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7621724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7627749	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7627756	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7629	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7629202	0.84[ASN][1000 genomes]
rs7629423	0.80[JPT][hapmap]
rs7631792	0.96[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap]
rs7634108	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs7634826	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs7640072	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7643779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7644453	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7645832	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7647873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9862595	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9968151	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]

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
rs1920642	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160284800-160295000	Weak transcription	Stomach Mucosa	stomach
2	chr3:160284800-160295200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:160285200-160294400	Weak transcription	HSMMtube	muscle
4	chr3:160285200-160298800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:160286800-160294800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr3:160286800-160295600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:160286800-160295800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:160286800-160301200	Weak transcription	HMEC	breast
9	chr3:160287000-160295600	Weak transcription	Adipose Nuclei	Adipose
10	chr3:160288000-160295400	Weak transcription	Psoas Muscle	Psoas
11	chr3:160288000-160295600	Weak transcription	Liver	Liver
12	chr3:160288200-160295600	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr3:160292200-160298800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:160292600-160295200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:160293600-160293800	Enhancers	HepG2	liver
16	chr3:160293600-160294800	Enhancers	Skeletal Muscle Male	skeletal muscle

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