Variant report

Variant	rs2053805
Chromosome Location	chr3:81738414-81738415
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:81732924..81735042-chr3:81736495..81738777,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11127740	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11707026	0.93[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11710970	0.82[EUR][1000 genomes]
rs11711331	0.84[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.97[TSI][hapmap]
rs12637814	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13062741	0.95[CEU][hapmap]
rs13065281	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13072957	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13073613	0.91[CEU][hapmap];0.97[GIH][hapmap];0.85[TSI][hapmap]
rs13079104	0.96[CEU][hapmap];0.97[GIH][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap]
rs13080520	0.91[CEU][hapmap];0.93[GIH][hapmap]
rs13086292	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13088603	0.86[EUR][1000 genomes]
rs13099615	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1464790	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.84[MEX][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap]
rs2229519	0.93[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28435942	0.82[EUR][1000 genomes]
rs3755713	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs3772882	0.80[CEU][hapmap];0.80[GIH][hapmap];0.81[TSI][hapmap]
rs3772883	0.80[CEU][hapmap];0.80[GIH][hapmap];0.81[TSI][hapmap]
rs3772884	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs3772891	0.81[JPT][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap]
rs3772896	0.87[CEU][hapmap];0.90[EUR][1000 genomes]
rs3772909	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3821548	0.88[CEU][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs3821551	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3821552	0.96[CEU][hapmap];0.90[YRI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3849570	0.84[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.97[TSI][hapmap]
rs3849571	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs3860595	0.80[CEU][hapmap]
rs3943556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4411908	0.80[CEU][hapmap];0.80[GIH][hapmap];0.81[TSI][hapmap]
rs6767749	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6795133	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7620240	0.88[CEU][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs7634258	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7642112	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9826069	0.90[EUR][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	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	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
5	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
6	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
7	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
8	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
9	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2053805	CADM2	cis	cerebellum	SCAN
rs2053805	GBE1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:45 , 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	chr3:81695400-81746200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr3:81699400-81766000	Weak transcription	NHLF	lung
8	chr3:81705400-81748000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr3:81712400-81746000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:81713000-81738800	Weak transcription	Left Ventricle	heart
11	chr3:81713000-81755200	Weak transcription	Lung	lung
12	chr3:81714400-81763600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:81714800-81751000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr3:81715800-81756200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:81718600-81757600	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr3:81726000-81755800	Strong transcription	Dnd41	blood
17	chr3:81726400-81762600	Weak transcription	HMEC	breast
18	chr3:81726600-81741200	Weak transcription	Gastric	stomach
19	chr3:81726600-81755200	Weak transcription	Pancreas	Pancrea
20	chr3:81726800-81766200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:81727000-81738800	Weak transcription	GM12878-XiMat	blood
22	chr3:81727200-81792200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr3:81727400-81754000	Weak transcription	Small Intestine	intestine
24	chr3:81728000-81755200	Weak transcription	Primary B cells from peripheral blood	blood
25	chr3:81730000-81738800	Weak transcription	Ovary	ovary
26	chr3:81730200-81739600	Weak transcription	Adipose Nuclei	Adipose
27	chr3:81731000-81747800	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr3:81732000-81766400	Weak transcription	HSMMtube	muscle
29	chr3:81733600-81748600	Weak transcription	Liver	Liver
30	chr3:81734200-81743600	Weak transcription	Psoas Muscle	Psoas
31	chr3:81734400-81747800	Weak transcription	Stomach Mucosa	stomach
32	chr3:81734600-81739600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:81734600-81741600	Weak transcription	Osteobl	bone
34	chr3:81734600-81749200	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr3:81734600-81752200	Weak transcription	HSMM	muscle
36	chr3:81734600-81765800	Weak transcription	HepG2	liver
37	chr3:81734800-81754400	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr3:81735400-81746200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:81735600-81764200	Weak transcription	A549	lung
40	chr3:81736200-81743400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr3:81737000-81738600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr3:81737000-81739600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:81737400-81738800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr3:81737400-81738800	Weak transcription	NHDF-Ad	bronchial
45	chr3:81737400-81762200	Weak transcription	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links