Variant report

Variant	rs4670210
Chromosome Location	chr2:37886901-37886902
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:37886213..37888801-chr2:37890844..37893237,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10694	0.87[CHB][hapmap];0.81[JPT][hapmap];0.92[MEX][hapmap];0.83[ASN][1000 genomes]
rs11124594	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11124595	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11883958	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12622958	0.90[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13387842	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13406302	0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17021174	0.82[ASN][1000 genomes]
rs2041508	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2072419	0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs3731852	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs3731854	0.87[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs4670211	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4670748	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56809883	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6544095	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67084656	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6709067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6709621	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6711909	0.91[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs6722589	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6740127	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6752119	0.87[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs6752220	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6752762	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6759224	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7607934	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7735	0.87[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.83[ASN][1000 genomes]
rs9742	0.87[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757793	chr2:37796654-38138939	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	esv2759043	chr2:37796654-38138939	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv833825	chr2:37808169-37985917	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv535645	chr2:37853282-37972640	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv535646	chr2:37853282-38014428	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv873880	chr2:37868214-37926046	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv535647	chr2:37874563-38014428	Enhancers Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv998567	chr2:37886244-37910627	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv963145	chr2:37886589-37890735	Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4670210	CDC42EP3	cis	cerebellum	SCAN
rs4670210	CDC42EP3	cis	lymphoblastoid	seeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37853600-37897400	Weak transcription	Small Intestine	intestine
2	chr2:37872000-37892400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr2:37873800-37889000	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr2:37874600-37893000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr2:37875800-37891800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr2:37875800-37893600	Weak transcription	Fetal Intestine Large	intestine
7	chr2:37875800-37896400	Weak transcription	Fetal Intestine Small	intestine
8	chr2:37878400-37894000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr2:37879600-37888800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr2:37879600-37893000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:37879600-37893000	Genic enhancers	Osteobl	bone
12	chr2:37879800-37888600	Weak transcription	Fetal Stomach	stomach
13	chr2:37880200-37888400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr2:37880400-37897000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr2:37881200-37890800	Enhancers	Rectal Smooth Muscle	rectum
16	chr2:37881400-37887600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr2:37881800-37893200	Genic enhancers	Primary neutrophils fromperipheralblood	blood
18	chr2:37881800-37893800	Genic enhancers	Primary monocytes fromperipheralblood	blood
19	chr2:37881800-37894200	Weak transcription	Fetal Muscle Trunk	muscle
20	chr2:37882000-37887000	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr2:37882000-37891400	Weak transcription	Primary hematopoietic stem cells	blood
22	chr2:37882400-37887600	Enhancers	Right Ventricle	heart
23	chr2:37882400-37895400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr2:37882600-37887400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
25	chr2:37882600-37887600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr2:37882600-37888000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr2:37882600-37888000	Genic enhancers	A549	lung
28	chr2:37882600-37896600	Weak transcription	Fetal Lung	lung
29	chr2:37882800-37888200	Genic enhancers	HSMMtube	muscle
30	chr2:37882800-37888800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr2:37882800-37896200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr2:37882800-37896400	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr2:37883200-37892400	Weak transcription	Fetal Brain Male	brain
34	chr2:37883200-37895400	Weak transcription	Brain Germinal Matrix	brain
35	chr2:37883400-37892000	Weak transcription	Fetal Brain Female	brain
36	chr2:37883400-37896400	Weak transcription	Colonic Mucosa	Colon
37	chr2:37883600-37887200	Genic enhancers	HMEC	breast
38	chr2:37883800-37887000	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr2:37884000-37891000	Enhancers	Colon Smooth Muscle	Colon
40	chr2:37884000-37893000	Weak transcription	Fetal Muscle Leg	muscle
41	chr2:37884400-37887000	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr2:37884400-37888800	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:37884400-37889400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
44	chr2:37884600-37887000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:37884600-37887000	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr2:37884600-37887000	Weak transcription	Psoas Muscle	Psoas
47	chr2:37884600-37887400	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr2:37884600-37888000	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr2:37884600-37888400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr2:37884600-37889000	Genic enhancers	NH-A	brain

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