Variant report

Variant	rs7640072
Chromosome Location	chr3:160257386-160257387
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160254211..160257700-chr3:160273142..160275155,4	MCF-7	breast:
2	chr3:160256295..160258095-chr3:160259329..160261299,2	K562	blood:
3	chr3:160251582..160254432-chr3:160256598..160258319,2	K562	blood:

Extended variants
information (count: 100 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10212236	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10513551	0.96[CEU][hapmap];0.83[CHB][hapmap];0.81[AMR][1000 genomes]
rs11706810	0.81[CEU][hapmap]
rs11918749	0.81[AMR][1000 genomes]
rs1317365	0.84[CEU][hapmap]
rs13403	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1451761	0.96[CEU][hapmap];0.83[CHB][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1451762	0.96[CEU][hapmap];0.83[CHB][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1451764	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1551190	0.84[CEU][hapmap];0.94[CHB][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1584688	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17236544	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17570467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1882126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1882127	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1920642	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1920657	0.83[JPT][hapmap]
rs1920662	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1920664	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2279457	0.96[CEU][hapmap];0.83[CHB][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2305407	0.91[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes]
rs2366969	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28705750	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2886825	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3732706	0.81[CEU][hapmap];0.88[JPT][hapmap]
rs3732707	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3773372	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3851365	0.81[CEU][hapmap];0.88[JPT][hapmap]
rs3851366	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4091703	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4292273	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4292274	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4621370	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4679654	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4679655	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4679885	0.96[CEU][hapmap];0.82[CHB][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4679888	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4679889	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4679890	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4679891	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4679896	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4679899	0.96[CEU][hapmap];0.94[CHB][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4679900	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4680579	0.96[CEU][hapmap];0.83[CHB][hapmap];0.81[AMR][1000 genomes]
rs4680580	0.96[CEU][hapmap];0.83[CHB][hapmap];0.80[AMR][1000 genomes]
rs4680585	0.96[CEU][hapmap];0.83[CHB][hapmap];0.84[EUR][1000 genomes]
rs4680587	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4680588	0.96[CEU][hapmap];0.83[CHB][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4680591	0.80[AMR][1000 genomes]
rs55731730	0.81[AMR][1000 genomes]
rs56156703	0.84[AMR][1000 genomes]
rs56197102	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56394279	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58322641	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60460891	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62272791	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62272792	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62272794	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272800	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272810	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6441314	0.96[CEU][hapmap];0.83[CHB][hapmap]
rs6441319	0.92[CEU][hapmap];0.83[CHB][hapmap]
rs6441320	0.96[CEU][hapmap];0.83[CHB][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6441324	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6768975	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6793560	0.92[CEU][hapmap];0.84[CHB][hapmap];0.81[AMR][1000 genomes]
rs6798183	0.80[CEU][hapmap]
rs6798668	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6801300	0.96[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6803828	0.92[CEU][hapmap];0.84[CHB][hapmap]
rs6806505	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6808083	0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6809153	0.81[CEU][hapmap]
rs6809313	0.81[CEU][hapmap]
rs721022	0.84[CEU][hapmap]
rs721023	0.96[CEU][hapmap];0.94[CHB][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7611130	0.96[CEU][hapmap];0.83[CHB][hapmap];0.81[AMR][1000 genomes]
rs7618974	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7621724	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7627749	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7627756	0.96[CEU][hapmap];0.94[CHB][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7629	0.96[CEU][hapmap];0.82[CHB][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7629202	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7631792	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7634108	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7634826	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7643779	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7644453	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7645832	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7647873	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9798898	0.81[AMR][1000 genomes]
rs9862595	0.96[CEU][hapmap];0.94[CHB][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9968151	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.80[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	nsv877701	chr3:160228001-160283815	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7640072	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160217400-160259600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:160219800-160263600	Weak transcription	Right Ventricle	heart
3	chr3:160220600-160261200	Weak transcription	Pancreas	Pancrea
4	chr3:160225600-160259800	Weak transcription	Stomach Mucosa	stomach
5	chr3:160234200-160258200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:160234600-160261000	Weak transcription	Spleen	Spleen
7	chr3:160234600-160281000	Weak transcription	Aorta	Aorta
8	chr3:160235000-160266600	Weak transcription	Esophagus	oesophagus
9	chr3:160239600-160265200	Weak transcription	Brain Substantia Nigra	brain
10	chr3:160240200-160280400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr3:160244200-160272200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:160244400-160263400	Weak transcription	Small Intestine	intestine
13	chr3:160244800-160259600	Weak transcription	Brain Angular Gyrus	brain
14	chr3:160245000-160258400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr3:160245000-160259800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr3:160245200-160262200	Weak transcription	Fetal Kidney	kidney
17	chr3:160246600-160279200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr3:160246800-160266400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr3:160247000-160258400	Weak transcription	HSMMtube	muscle
20	chr3:160247000-160259800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr3:160247000-160261000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr3:160247000-160270400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr3:160247000-160281000	Weak transcription	Thymus	Thymus
24	chr3:160248400-160261200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:160248400-160261200	Weak transcription	Gastric	stomach
26	chr3:160248400-160261200	Weak transcription	Lung	lung
27	chr3:160248400-160261200	Weak transcription	Ovary	ovary
28	chr3:160248400-160261600	Weak transcription	Fetal Stomach	stomach
29	chr3:160248800-160263000	Weak transcription	Brain Hippocampus Middle	brain
30	chr3:160248800-160268600	Weak transcription	NHLF	lung
31	chr3:160249200-160261200	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr3:160249200-160279000	Weak transcription	Stomach Smooth Muscle	stomach
33	chr3:160249800-160261600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr3:160250400-160258400	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr3:160250400-160271600	Weak transcription	HepG2	liver
36	chr3:160250600-160259400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr3:160251000-160258400	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr3:160251000-160266800	Weak transcription	Primary hematopoietic stem cells	blood
39	chr3:160251200-160261000	Weak transcription	Left Ventricle	heart
40	chr3:160251200-160282000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr3:160251600-160263400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr3:160251800-160263000	Weak transcription	GM12878-XiMat	blood
43	chr3:160252200-160260000	Weak transcription	A549	lung
44	chr3:160252400-160267200	Weak transcription	Primary B cells from cord blood	blood
45	chr3:160252800-160258600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr3:160252800-160259000	Weak transcription	Fetal Thymus	thymus
47	chr3:160252800-160261200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr3:160252800-160272600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr3:160253000-160258200	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr3:160253000-160258400	Weak transcription	H1 Cell Line	embryonic stem cell

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