Variant report

Variant	rs1375086
Chromosome Location	chr3:81728517-81728518
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11127737	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1155277	0.96[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11711331	0.80[GIH][hapmap]
rs1972976	0.87[EUR][1000 genomes]
rs2372908	0.86[MEX][hapmap]
rs2594547	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2594549	0.96[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2594551	1.00[CEU][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2594553	0.96[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2594562	0.96[CEU][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2680245	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2680257	0.96[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2680260	1.00[JPT][hapmap]
rs2680264	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2680277	0.91[CEU][hapmap];1.00[YRI][hapmap]
rs2680280	0.96[CEU][hapmap];0.88[JPT][hapmap]
rs2691093	0.92[CEU][hapmap];0.86[GIH][hapmap]
rs3107240	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3772882	0.84[GIH][hapmap]
rs3772883	0.84[GIH][hapmap]
rs3772889	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3772899	0.92[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs3772902	0.92[CEU][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs3772914	0.86[MEX][hapmap]
rs3821548	0.80[GIH][hapmap]
rs3849570	0.80[GIH][hapmap]
rs3860595	0.89[GIH][hapmap]
rs4411908	0.84[GIH][hapmap]
rs6771266	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6785616	0.86[MEX][hapmap]
rs6800135	0.86[MEX][hapmap]
rs6803932	0.96[CEU][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap]
rs7648237	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9309876	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9818090	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838088	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9846154	0.86[MEX][hapmap]
rs9852545	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9860805	0.90[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9869348	0.86[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933756	chr3:81413060-81754738	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1003217	chr3:81435044-81752521	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1012133	chr3:81499082-81817471	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv933259	chr3:81523854-81730617	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv949545	chr3:81523898-81893929	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv1009607	chr3:81651419-81825151	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv536604	chr3:81651419-81825151	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv834749	chr3:81655377-81818880	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv999992	chr3:81693662-82015969	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
10	nsv536605	chr3:81693662-82015969	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1375086	CADM2	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:81627400-81755000	Weak transcription	Primary B cells from cord blood	blood
2	chr3:81642000-81753000	Weak transcription	HUVEC	blood vessel
3	chr3:81689600-81744000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr3:81689800-81744000	Weak transcription	Right Ventricle	heart
5	chr3:81695200-81748000	Weak transcription	Aorta	Aorta
6	chr3:81695400-81733800	Weak transcription	HSMM	muscle
7	chr3:81695400-81746200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:81699400-81766000	Weak transcription	NHLF	lung
9	chr3:81705400-81748000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr3:81709800-81733400	Weak transcription	Fetal Intestine Small	intestine
11	chr3:81712400-81746000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:81712800-81730000	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr3:81713000-81738800	Weak transcription	Left Ventricle	heart
14	chr3:81713000-81755200	Weak transcription	Lung	lung
15	chr3:81714000-81729400	Weak transcription	Adipose Nuclei	Adipose
16	chr3:81714400-81763600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr3:81714800-81751000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr3:81715800-81756200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:81718000-81734000	Weak transcription	Osteobl	bone
20	chr3:81718000-81735000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr3:81718600-81729200	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr3:81718600-81757600	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr3:81718800-81728600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:81719600-81733200	Weak transcription	NHDF-Ad	bronchial
25	chr3:81719600-81734000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr3:81726000-81755800	Strong transcription	Dnd41	blood
27	chr3:81726200-81730600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:81726400-81762600	Weak transcription	HMEC	breast
29	chr3:81726600-81731000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:81726600-81734200	Weak transcription	Duodenum Mucosa	Duodenum
31	chr3:81726600-81741200	Weak transcription	Gastric	stomach
32	chr3:81726600-81755200	Weak transcription	Pancreas	Pancrea
33	chr3:81726800-81766200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr3:81727000-81733600	Weak transcription	Psoas Muscle	Psoas
35	chr3:81727000-81738800	Weak transcription	GM12878-XiMat	blood
36	chr3:81727200-81733000	Weak transcription	A549	lung
37	chr3:81727200-81733200	Weak transcription	Liver	Liver
38	chr3:81727200-81734000	Weak transcription	HepG2	liver
39	chr3:81727200-81792200	Weak transcription	Primary hematopoietic stem cells	blood
40	chr3:81727400-81754000	Weak transcription	Small Intestine	intestine
41	chr3:81728000-81755200	Weak transcription	Primary B cells from peripheral blood	blood
42	chr3:81728400-81729200	Strong transcription	Muscle Satellite Cultured Cells	--
43	chr3:81728400-81730800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr3:81728400-81735000	Weak transcription	Stomach Smooth Muscle	stomach

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